Verification of TMDOCK generated dimers for consistency to experimental data

Parallel homodimers of bitopic proteins included into the Membranome 2.0 database were generated by the TMDOCK method [1]. The accuracy and reliability of TMDOCK predictions has been previously justified by successful prediction of 26 experimental structures of homodimers with r.m.s.d. below 3.3 Å.

TMDOCK predicts not only functionally relevant dimers, but also transient dimers formed due to high propensity TM α-helices of bitopic proteins to aggregate in the lipid bilayer. For 6,039 bitopic proteins from the database, TMDOCK predicted 5,670 homodimers with ΔGasc< -1kcal/mol and 4,858 homodimers with ΔGasc<-3 kcal/mol. To select functionally relevant dimers, we used the following criteria: (a) a sufficient stability of calculated dimers (ΔGasc<-3kcal/mol); (b) an adequate calculated hydrophobic thickness of the dimer that differ from average thickness of residence membrane by less than 6Å; (c) arrangement of highly polar residues (N, D, Q, E, R, K, H) at helix-helix interface to form interhelical hydrogen bonds; (d) close packing of TM α-helices; and (e) conservation of the helix packing mode in a number of proteins from the same superfamily. Based on these criteria, 2,130 homodimers were included into the Membranome database.

The included dimers were further verified for consistency to published experimental data on homodimerization of 557 bitopic proteins (Tables 1-5). These data include: (a) helix association modes proposed based on from NMR or mutagenesis experiments for 53 dimers (Table 1 and 2); (b) evidence of TM helix association by TOXCAT or other methods for 185 proteins (Table 3); (c) crystal structures of homodimers of water-soluble domains of 161 different bitopic proteins (Table 4); and (d) UniProt annotation of 304 bitopic proteins as forming homodimers (Table 5).

Table 1. Bitopic proteins from Membranome 2.0 with experimentally determined 3D models of transmembrane homodimers
Family code Protein name UniProt code References PDB1 Type2 Comment3 Beta-type
platelet-derived growth
factor receptor
PGFRB_HUMAN [2, 3, 4, 5] 2l6w L -(R)4 Epidermal growth factor
EGFR_HUMAN [2, 6, 7, 8, 9, 10, 11, 12, 13] 2m0b, 2m20 R + Receptor
tyrosine-protein kinase
ERBB2_HUMAN [2, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] 2jwa, 2n2a R + Receptor
tyrosine-protein kinase
ERBB3_HUMAN [2, 8, 9, 12, 13, 21] 2l9u L -(R)4 Receptor
tyrosine-protein kinase
ERBB4_HUMAN [2, 8, 9, 12, 13] 2l2t R + Ephrin type-A receptor 1 EPHA1_HUMAN [2, 22] 2k1k, 2k1l R + Ephrin type-A receptor 2 EPHA2_HUMAN [2, 23] 2k9y L -(R)4 Fibroblast growth factor
receptor 3
FGFR3_HUMAN [2, 24, 25, 26, 27] 2lzl L -(R)4 Vascular endothelial
growth factor receptor 2
VGFR2_HUMAN [2, 28] 2m59, 2meu L + Tumor necrosis factor
receptor superfamily
member 16
TNR16_HUMAN [29, 30, 31] 2mic, 2mjo L +5 Toll-like receptor 3 TLR3_HUMAN [32, 33] 2mka, 2mk9 R, L + T-cell surface
glycoprotein CD3 zeta
CD3Z_HUMAN [34] 2hac L + Amyloid beta A4 protein A4_HUMAN [35, 36, 37, 38, 39, 40, 41] 2lz3, 2lz4, 2loh R, L + TYRO protein tyrosine
kinase-binding protein
TYOBP_HUMAN [42, 43] 2l34, 4wo1, 4wol L + Glycophorin-A GLPA_HUMAN [44, 45, 46, 47] [48, 49, 50, 51] 5eh4 R + BCL2/adenovirus E1B 19
kDa protein-interacting
protein 3
BNIP3_HUMAN [52, 53, 54, 55, 56] 2ka1, 2ka2, 2j5d R +

1 Representative PDB files for significantly different 3D structures

2 Type of the dimeric association in NMR models: “L” is left handed Leu-zipper-like association with helix crossing angle of +10 to +30°; “R” is right-handed association through GXXXG-like motif with helix crossing angle of -60 to -30°

3 Sign “+” indicates that the predicted structures were roughly consistent with experimental models

4 The calculated preferable helix arrangement was “R” through GXXXG motif, just as for most other homologous proteins from the same family. The NMR-like models with left-handed helix arrangement were also generated in calculations, but they had a higher association energy

5 The sets of calculated low-energy association modes are partly different for human and rat sequences. The 3D models of homodimer included in Membranome were calculated for rat sequence to facilitate comparison with NMR model from the PDB (2mic).

Table 2. Bitopic proteins from Membranome with specific modes of transmembrane homodimerization suggested in the literature based on experimental data.
Family code Protein name Type1 UniProt code References Comment2 Receptor-type tyrosine-protein
phosphatase eta
R PTPRJ_HUMAN [57] + Erythropoietin receptor L EPOR_HUMAN [58, 59, 60, 61] +3 Thrombopoietin receptor L TPOR_HUMAN [62, 63, 64] + T-cell surface glycoprotein CD4 R CD4_HUMAN [65] +4 Carcinoembryonic
antigen-related cell adhesion
molecule 1
R CEAM1_HUMAN [66, 67, 68] + Proto-oncogene tyrosine-protein
kinase receptor Ret
L RET_HUMAN [2, 69, 70] + Atypical kinase ADCK3,
L ADCK3_HUMAN [71] + AarF domain-containing protein
kinase 4
L ADCK4_HUMAN [71] + Leucine-rich repeat receptor-like
kinase SOBIR1
R SBIR1_ARATH [72] + Serine/threonine-protein
kinase-like protein ACR4
L ACR4L_ARATH [73, 74] + Epithelial discoidin
domain-containing receptor 1
L DDR1_HUMAN [2, 68, 75] + Integrin alpha-IIb R ITA2B_HUMAN [76, 77, 78, 79] + Integrin beta-3 R ITB3_HUMAN [80, 81] -5 Neuropilin-1 R NRP1_HUMAN [12, 82, 83] + Kit ligand L SCF_HUMAN [84] + Plexin-D1 L PLXD1_HUMAN [85] + Syndecan-2 R SDC2_HUMAN [86, 87, 88] + Syndecan-3 R SDC3_HUMAN [88, 89] + Syndecan-4 R SDC4_HUMAN [86, 88] + Platelet glycoprotein Ib beta chain L GP1BB_HUMAN [90, 91] + HLA class II histocompatibility
antigen, DRB1-15 beta chain
R 2B1F_HUMAN [92] + HLA class II histocompatibility
antigen, DRB1-10 beta chain
R 2B1A_HUMAN [93] + HLA class II histocompatibility
antigen, DRB1-1 beta chain
R 2B11_HUMAN [92] + HLA class II histocompatibility
antigen, DQ alpha 1 chain
R DQA1_HUMAN [68, 92] +6* B-cell antigen receptor
complex-associated protein beta
L CD79B_HUMAN [94] + CD40 ligand R,L CD40L_HUMAN [94] +(no) Myelin protein P0 R MYP0_HUMAN [68, 95] + Cadherin-1 R CADH1_HUMAN [96] -7 P-selectin R LYAM3_HUMAN [97] + Cell division protein FtsB L FTSB_ECOLI [98, 99] + Sec-independent protein
translocase protein TatA
L TATA_ECOLI [100] +8 Vesicle-associated membrane
protein 2
L VAMP2_HUMAN [101, 102, 103, 104, 105] + Sodium/potassium-transporting
ATPase subunit beta-1
R AT1B1_HUMAN [106] + Cytochrome b559 subunit beta R PSBF_ARATH [107, 108, 109] + Sulfhydryl oxidase 2 L QSOX2_HUMAN [110, 111] + Galactoside
3(4)-L-fucosyltransferase 3
L FUT3_HUMAN [94] + Dipeptidyl peptidase 4 R DPP4_HUMAN [112] +

1 Type of helix arrangement in calculated models: L, left handed; R, right handed

2 Sign “+” indicates that the calculated model was consistent with experimental data; “+(no)” indicates that experimental-like model was generated by TMDOCK, but not included in the Membranome database due to inconsistency with criteria for selection of functional structures

3 Mode of association was changed when calculated for a different sequence used in experimental study [58 14602718] and became consistent with interface identified by Asn-scanning mutagenesis.

4 Experimental study was conducted for mouse orthologue with slightly different sequence. The results of calculations with TMDOCK are consistent with experimental findings that Gly mutation does not affect the strength of dimerization, but leads to the loss of function. According to calculations, the helices remain strongly associated in the mutant, but switch from R-type to L-type of the dimer.

5 The model was consistent only with a small subset of interfacial residues proposed in the experimental study. The discrepancies could be due to multiple modes of association found for the transmembrane helices including formation of a homotrimer [80].

6 Calculations show multiple association modes through different pairs of small residues.

7 TOXCAT studies were performed for the shorter TM segment and indicated L-type dimerization mode [96], while calculations for longer sequence resulted in the best dimers with R-type of dimerization, similar to other family members

8 Structure of TMDOCK-generated homodimer is stabilized by interactions of Gln8 residues that was found to be functionally important [100], but it differs from the NMR-derived structure of nonamer (2lzs)

Table 3. Bitopic proteins from Membranome whose TM segments were studied for homo-dimerization by TOXCAT or other direct experimental methods, in addition to proteins included in Tables 1 and 2.
Family code Protein name Type UniProt code References Exp. Calc.1 Receptor-type tyrosine-protein phosphatase C R PTPRC_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase delta R PTPRD_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase F R PTPRF_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase gamma L PTPRG_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase S R PTPRS_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase zeta L PTPRZ_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase H R PTPRH_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase O L PTPRO_HUMAN [57, 113] + + Receptor-type tyrosine-protein phosphatase alpha L PTPRA_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase epsilon L PTPRE_HUMAN [57] + + Phosphatidylinositol
phosphatase PTPRQ
R PTPRQ_HUMAN [57] + + Receptor-type tyrosine-protein
phosphatase R
R PTPRR_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase N2 R PTPR2_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase N R PTPRN_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase kappa R PTPRK_HUMAN [57, 68] + + Receptor-type tyrosine-protein phosphatase mu R PTPRM_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase T R PTPRT_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase U R PTPRU_HUMAN [57] + + Receptor-type tyrosine-protein phosphatase beta R PTPRB_HUMAN [57] w +w Fc receptor-like protein 3 R FCRL3_HUMAN [111] + + Prolactin receptor R PRLR_HUMAN [114] + + Interleukin-12 receptor subunit beta-1 R I12R1_HUMAN [115] + + Interleukin-6 receptor subunit beta L IL6RB_HUMAN [116] + + Interleukin-27 receptor subunit alpha L I27RA_HUMAN [68] + +(no) Interleukin-6 receptor subunit beta R IL6RA_HUMAN [116] + + Interleukin-2 receptor subunit beta R IL2RB_HUMAN [117] + + Cytokine receptor common subunit gamma L IL2RG_HUMAN [117] + + Interleukin-9 receptor R IL9R_HUMAN [117] + +(no) Leukocyte immunoglobulin-like receptor subfamily B member 1 R LIRB1_HUMAN [68] + + Killer cell immunoglobulin-like receptor 2DL5A L KI2LA_HUMAN [68] + + Killer cell immunoglobulin-like receptor 2DS1 R KI2S1_HUMAN [68] + + Killer cell immunoglobulin-like receptor 3DL1 L KI3L1_HUMAN [68] + + CMRF35-like molecule 8 L CLM8_HUMAN [68] + + Polymeric immunoglobulin receptor R PIGR_HUMAN [118] + + Macrophage colony-stimulating factor 1 receptor L CSF1R_HUMAN [2] + + Receptor-type tyrosine-protein kinase FLT3 R FLT3_HUMAN [2] + + Mast/stem cell growth factor receptor Kit L KIT_HUMAN [2] + + Platelet-derived growth factor receptor alpha R PGFRA_HUMAN [2] + + Ephrin type-A receptor 3 R EPHA3_HUMAN [2] + + Amyloid beta A4 protein R EPHA4_HUMAN [2] + + Ephrin type-A receptor 5 R EPHA5_HUMAN [2] + + Ephrin type-A receptor 6 R EPHA6_HUMAN [2] + + Ephrin type-A receptor 7 R EPHA7_HUMAN [2] + + Ephrin type-A receptor 8 R EPHA8_HUMAN [2] + + R EPHAA_HUMAN [2] + + Ephrin type-A receptor 10 R EPHB1_HUMAN [2] + + Ephrin type-B receptor 1 R EPHB2_HUMAN [2] + + Ephrin type-B receptor 2 R EPHB3_HUMAN [2] + + Ephrin type-B receptor 3 R EPHB4_HUMAN [2] + + Ephrin type-B receptor 4 R EPHB4_HUMAN [2] + + Ephrin type-B receptor 6 R EPHB6_HUMAN [2] + + Fibroblast growth factor receptor 1 R FGFR1_HUMAN [2, 119] + + Fibroblast growth factor receptor 2 R FGFR2_HUMAN [2, 26, 120] + + Fibroblast growth factor receptor 4 R FGFR4_HUMAN [2] + + Insulin-like growth factor 1 receptor R IGF1R_HUMAN [2] + + Insulin receptor R INSR_HUMAN [2, 29, 121, 122] + + Insulin receptor-related protein R INSRR_HUMAN [2, 29, 123] + + Tyrosine-protein kinase transmembrane receptor ROR1 L ROR1_HUMAN [2] + +(no) Tyrosine-protein kinase transmembrane receptor ROR2 L ROR2_HUMAN [2] + +(no) Tyrosine-protein kinase receptor Tie-1 L TIE1_HUMAN [2, 122] + + Angiopoietin-1 receptor L TIE2_HUMAN [2, 122] + + Tyrosine-protein kinase Mer R MERTK_HUMAN [2] + + Tyrosine-protein kinase receptor TYRO3 R TYRO3_HUMAN [2] + + Tyrosine-protein kinase receptor UFO R UFO_HUMAN [2] + + Hepatocyte growth factor receptor R MET_HUMAN [2] + + Macrophage-stimulating protein receptor L RON_HUMAN [2] + + Serine/threonine-protein kinase LMTK1 L LMTK1_HUMAN [2] + + Serine/threonine-protein kinase LMTK2 L LMTK2_HUMAN [2] + + Serine/threonine-protein kinase LMTK3 R LMTK3_HUMAN [2] + + Serine/threonine-protein kinase/endoribonuclease IRE1 L ERN1_HUMAN [124] + + Vascular endothelial growth factor receptor 1 L VGFR1_HUMAN [2] + + Vascular endothelial growth factor receptor 3 L VGFR3_HUMAN [2] + + Muscle, skeletal receptor tyrosine protein kinase R MUSK_HUMAN [2] + + Tyrosine-protein kinase RYK R RYK_HUMAN [2, 125] + + Tyrosine-protein kinase STYK1 R STYK1_HUMAN [2] + + Atrial natriuretic peptide receptor A L ANPRA_HUMAN [126] + + Discoidin domain-containing receptor 2 L DDR2_HUMAN [2] + + High affinity nerve growth factor receptor R NTRK1_HUMAN [2, 127] + + BDNF/NT-3 growth factors receptor R NTRK2_HUMAN [2, 127] + + NT-3 growth factor receptor R NTRK3_HUMAN [2] + + ALK tyrosine kinase receptor L ALK_HUMAN [2] + + Leukocyte tyrosine kinase receptor R LTK_HUMAN [2, 122] + + Inactive tyrosine-protein kinase 7 R PTK7_HUMAN [2] + + Proto-oncogene tyrosine-protein kinase ROS R ROS1_HUMAN [2] + +(no) Macrosialin - CD68_HUMAN [68] - - C-type lectin domain family 10 member A L CLC10_HUMAN [68, 111] + + C-type lectin domain family 10 member A L CL12A_HUMAN [111] + + C-type lectin domain family 4 member D L CLC4D_HUMAN [111] + + Chondrolectin R CHODL_HUMAN [111] + + Stabilin-1 R STAB1_HUMAN [99] + + Apical endosomal glycoprotein L AEGP_HUMAN [68] + + Toll-like receptor 1 L TLR1_HUMAN [32] + + Toll-like receptor 2 L TLR2_HUMAN [32] + + Toll-like receptor 3 L TLR3_HUMAN [32] + + Toll-like receptor 4 L TLR4_HUMAN [32] + + Toll-like receptor 5 L TLR5_HUMAN [32] + + Toll-like receptor 6 L TLR6_HUMAN [32] + + Toll-like receptor 7 L TLR7_HUMAN [32] + + Toll-like receptor 8 L TLR8_HUMAN [32] + + Toll-like receptor 9 R TLR9_HUMAN [32, 129] + + Toll-like receptor 10 L TLR10_HUMAN [32] + + Integrin alpha-M R, L ITA7_HUMAN [130] + +(no) Integrin alpha-7 R ITA7_HUMAN [68] + + Integrin alpha-1 L, R ITA1_HUMAN [68] + +(no) Integrin beta-1 L, R ITB1_HUMAN [68] + + Integrin beta-2 R ITB2_HUMAN [130] + +(no) Anthrax toxin receptor 1 L ANTR1_HUMAN [131] + + Neuropilin-2 L NRP2_HUMAN [12] + + Plexin-A1 R PLXA1_HUMAN [12, 83] + + Plexin-B1 R PLXB1_HUMAN [12] + + Plexin-A2 L PLXA2_HUMAN [12] + + Amyloid beta A4 protein R PLXA4_HUMAN [132] + + Syndecan-1 R SDC1_HUMAN [88] + + Leucine-rich repeat-containing protein 32 L LRC32_HUMAN [111] + + SLIT and NTRK-like protein 4 R SLIK4_HUMAN [68] + + Platelet glycoprotein Ib alpha chain L, R GP1BA_HUMAN [91] - +(no) Platelet glycoprotein IX R GPIX_HUMAN [91] - +w HLA class I histocompatibility antigen, A-2 alpha chain R 1A02_HUMAN [68] + + HLA class II histocompatibility antigen, DO beta chain R DOB_HUMAN [68] + + HLA class II histocompatibility antigen, DP alpha 1 chain L DPA1_HUMAN [68] + + HLA class II histocompatibility antigen, DO alpha chain R DOA_HUMAN [68] + + HLA class II histocompatibility antigen, DM alpha chain R DMA_HUMAN [68] + + HLA class II histocompatibility antigen gamma chain L HG2A_HUMAN [133, 134] + + B-cell antigen receptor complex-associated protein alpha chain - CD79A_HUMAN [94] - - Neuropilin and tolloid-like protein 2 R NETO2_HUMAN [133, 134] + + Protein GAPT L GAPT_HUMAN [68] + + Mucin-4 R MUC4_HUMAN [12, 13] + + Sialic acid-binding Ig-like lectin 7 R SIGL7_HUMAN [68] + + Myeloid cell surface antigen CD33 R CD33_HUMAN [68] + + Sialic acid-binding Ig-like lectin 11 R SIG11_HUMAN [68] + + Coxsackievirus and adenovirus receptor R CXAR_HUMAN [68] + + CXADR-like membrane protein R CLMP_HUMAN [68] + + Neural cell adhesion molecule L1 R L1CAM_HUMAN [12] + + Kin of IRRE-like protein 3 R KIRR3_HUMAN [68] + + Cell adhesion molecule 2 R CADM2_HUMAN [68] + + Cell adhesion molecule 3 R CADM3_HUMAN [68] + + Cadherin-24 R CAD24_HUMAN [68] + + Cadherin-3 R CADH3_HUMAN [68] + + Cadherin-7 R CADH7_HUMAN [68] + + Calsyntenin-1 L CSTN1_HUMAN [111] + + Desmoglein-2 L DSG2_HUMAN [68] + + Protocadherin gamma-B4 L PCDGG_HUMAN [68] + + Epsilon-sarcoglycan L SGCE_HUMAN [111] + + Bone marrow stromal antigen 2 L BST2_HUMAN [135] + + Leucine-rich repeat TM neuronal protein 3 L LRRT3_HUMAN [111] + + Leucine-rich repeat and fibronectin type-III domain-containing protein 4 R LRFN4_HUMA [68] + + L-selectin L LYAM1_HUMAN [136] - +w2 Multiple epidermal growth factor-like domains protein 9 R MEGF9_HUMAN [68] + + Nesprin-1 L SYNE1_HUMAN [68] + + Cell division protein ZipA R, L ZIPA_ECOLI [99] + +(no) Cell division protein FtsL L FTSL_ECOLI [99] + + Cell division protein FtsQ L FTSQ_ECOLI [99] + +(no) Cell division protein FtsN L FTSN_ECOLI [99] + + DnaJ-like protein DjlA R DJLA_ECOLI [137] + + Protein ROT1 R, L ROT1_YEAST [138] - +(no) Syntaxin-1A R STX1A_HUMAN [102, 103, 105] + +(no) Syntaxin-2 L STX2_HUMAN [68] + + Vesicle-associated membrane protein 1 R VAMP1_HUMAN [68] + + Vesicle-associated membrane protein 4 L VAMP4_HUMAN [105] + +(no) Dysferlin L DYSF_HUMAN [111] + +(no) Melanocyte protein PMEL L PMEL_HUMAN [139] + + Sodium/potassium-transporting ATPase subunit gamma L PMEL_HUMAN [68, 140] + +(no) Cardiac phospholamban L PPLA_HUMAN [141, 142, 143] + +(no) Calcium-activated chloride channel regulator 2 L CLCA2_HUMAN [111] + +(no) Phospholipid scramblase 1 L PLS1_HUMAN [144] - +(no) V-type proton ATPase subunit S1 L VAS1_HUMAN [99] + +(no) ATP synthase subunit g, mitochondrial L ATP5L_HUMAN [145] + +(no) Transmembrane protein 132B L T132B_HUMAN [68] + +(no) Transcriptional activator CadC R CADC_ECOLI [146] - +3* Beta-1,4 N-acetylgalactosaminyltransferase 2 L B4GN2_HUMAN [111] + + UDP-glucuronosyltransferase 2B11 R UDB11_HUMAN [68] + + Diacylglycerol kinase epsilon L DGKE_HUMAN [147] + + Peptidoglycan synthase FtsI L FTSI_ECOLI [99] + +(no) Transmembrane protease serine 11D L TM11D_HUMAN [68] + + Furin L FURIN_HUMAN [68] + + Neuropathy target esterase R PLPL6_HUMAN [68] + + Patatin-like phospholipase domain-containing protein 7 R PLPL7_HUMAN [68] + + Sperm acrosome membrane-associated protein 1 R SACA1_HUMAN [68] + + Apoptosis regulator BAX L BAX_HUMAN [148] + + Chloride intracellular channel protein 1 L CLIC1_HUMAN [149, 150] + +(no) E3 ubiquitin-protein ligase RNF144B L R144B_HUMAN [68] + +(no) Ubiquitin-conjugating enzyme E2 J2 L, R UB2J2_HUMAN [111] + +(no) Protein FAM69A R FA69A_HUMAN [111] + + Protein FAM173B L F173B_HUMAN [99] + + Putative uncharacterized protein C8orf49 R CH049_HUMAN [68] + + Leucine-rich repeat and transmembrane domain-containing protein 2 L LRTM2_HUMAN [68] + + Protein ARMCX6 R ARMX6_HUMAN [68] + +

1 See footnotes for Table 2. “w” indicates very weak association biased on TOXCAT data (for “Exp.” column) or calculated free energy of association (for “Calc.” column).

2 The predicted association is weak (-4 kcal/mol); some data indicate at possible dimerization.

3 Experimental study concluded that TM domain of CadC was not significantly involved in dimerization. However, TMDOCK modeling suggests formation of an R-type TM homodimer through GxxxG-like motif, similar to many other proteins with receptor-like organization.

Table 4. Bitopic proteins from Membranome with biologically relevant crystal structures of homodimers formed by water-soluble domains.
Family code Protein PDB code UniProt code Comment1 Receptor-type tyrosine-protein phosphatase O 2gjt PTPRO_HUMAN + * Receptor-type tyrosine-protein phosphatase N 2qt7 PTPRN_HUMAN + * IgE receptor, alpha chain 1rpq FCERA_HUMAN + Erythropoietin receptor 1ern EPOR_HUMAN + * Interleukin-6 receptor subunit beta 1bqu IL6RB_HUMAN + * Leptin receptor 3v6o LEPR_HUMAN + Cytokine receptor common subunit beta 1gh7 IL3RB_HUMAN + Interleukin-7 receptor subunit alpha 3up1 IL7RA_HUMAN + BTN3A1 ectodomain 4f9l BT3A1_HUMAN + Programmed cell death 1 ligand 1 3fn3 PD1L1_HUMAN + Leukocyte-associated Ig-like receptor 1 4esk LAIR1_HUMAN + Leukocyte immunoglobulin-like receptor A2 2otp LIRA2_HUMAN + Leukocyte immunoglobulin-like receptor B1 1vdg LIRB1_HUMAN + * Platelet glycoprotein VI 2gi7 GPVI_HUMAN +(no) Triggering receptor expressed on myeloid cells 1 1q8m TREM1_HUMAN + Natural cytotoxicity triggering receptor 3 3noi NCTR3_HUMAN + Basigin 3qqn BASI_HUMAN +(no) Glycoprotein cd8 alpha chain 2hp4 CD8A_HUMAN + CD2 antigen 1hng CD2_HUMAN + SLAM family member 5 2pkd SLAF5_HUMAN +(no) SLAM family member 6 2if7 SLAF6_HUMAN + Signal-regulatory protein gamma 4i2x SIRPG_HUMAN + Tyrosine-protein phosphatase non-receptor type substrate 1 2uv3 SHPS1_HUMAN + Netrin receptor UNC5B 1wmg UNC5B_HUMAN + CEAM1 4qxw CEAM1_HUMAN + * Cytotoxic T lymphocyte associated antigen 4 3osk CTLA4_HUMAN + * T-cell receptor beta-1 chain C region 2axh TRBC1_HUMAN + Myotonic dystrophy protein kinase 2vd5 DMPK_HUMAN + Mast/stem cell growth factor receptor Kit 2e9w KIT_HUMAN + * Ephrin type-b receptor 2 1b4f EPHB2_HUMAN + * Fibroblast growth factor receptor 1 1fgk FGFR1_HUMAN + * Fibroblast growth factor receptor 2 2psq FGFR2_HUMAN + * Insulin receptor 2hr7 INSR_HUMAN + * Tyrosine-protein kinase transmembrane receptor ROR2 3zzw ROR2_HUMAN +(no) * Hepatocyte growth factor receptor 3efj MET_HUMAN + * Proto-oncogene tyrosine-protein kinase receptor RET 2ivs RET_HUMAN + * Kinase/endoribonuclease 3p23 ERN1_HUMAN + * Serine/threonine-protein kinase/endoribonuclease IRE1 2rio IRE1_YEAST + Vascular endothelial growth factor receptor 1 4cl7 VGFR1_HUMAN + * Muscle, skeletal receptor tyrosine protein kinase 3hkl MUSK_HUMAN + * Hormone binding domain of the atrial natriuretic receptor 1dp4 ANPRA_HUMAN + * Macrophage receptor MARCO 2oya MARCO_HUMAN +(no) C-type lectin 2D 4qkh CLC2D_HUMAN + C-type lectin 4C 3wbp CLC4C_HUMAN + C-type lectin 4D 3whd CLC4D_HUMAN + * C-type lectin 4M 1k9j CLC4M_HUMAN + C-type lectin 7A 2bpd CLC7A_HUMAN + Early activation antigen cd69 3hup CD69_HUMAN + Immunoglobulin epsilon FC receptor 4gi0 FCER2_HUMAN + Killer cell lectin-like receptor subfamily G member 1 3ff9 KLRG1_HUMAN + Macrophage mannose receptor 1 1egg KLRG1_HUMAN + Oxidized low-density lipoprotein receptor 1 1ypq OLR1_HUMAN + Tumor necrosis factor receptor 1A 1ext TNR1A_HUMAN + Tumor necrosis factor receptor 11A 3me4 TNR11_HUMAN + Toll-like receptor 10 2j67 TLR10_HUMAN + * Toll-like receptor 2 1o77 TLR2_HUMAN Toll-like receptor 5 3j0a TLR5_HUMAN + * Toll-like receptor 6 4om7 TLR6_HUMAN + * Toll-like receptor 8 3w3n TLR8_HUMAN + * Plexin-A2 3al9 PLXA2_HUMAN + * Plexin-B1 2r2o PLXB1_HUMAN + * Plexin-C1 3kuz PLXC1_HUMAN + Syndecan-4 1ejp SDC4_HUMAN + * Neurogenic locus notch homolog protein 1 2he0 NOTC1_HUMAN + Amyloid-like protein 1 3pmr APLP1_HUMAN + T-cell antigen receptor alpha-beta complex 3of6 PTCRA_HUMAN +(no) CD44 antigen 4pz3 CD44_HUMAN + Ig mu chain C region 4jvu IGHM_HUMAN + B-cell antigen receptor 3kho CD79B_HUMAN + * Semaphorin-4D 1olz SEM4D_HUMAN + Semaphorin-6A 3okw SEM6A_HUMAN + Neuroligin-2 3bl8 NLGN2_HUMAN + Neuroligin-4 3be8 NLGNX_HUMAN + Seuroligin-1 3bix NLGN1_HUMAN + Fms-related tyrosine kinase 3 ligand 1ete FLT3L_HUMAN + KIT ligand 1scf SCF_HUMAN + * Fibronectin type III domain-containing protein 5 4lsd FNDC5_HUMAN +(no) Macrophage colony-stimulating factor 1 4fa8 CSF1_HUMAN + Fractalkine 1f2l X3CL1_HUMAN +(no) Modulator protein MzrA 4pwu MZRA_ECOLI + Coxsackie virus and adenovirus receptor 1eaj CXAR_HUMAN + * Junctional adhesion molecule A 1nbq JAM1_HUMAN + Kin of IRRE-like protein 1 4ofd KIRR1_HUMAN + Amphoterin-induced protein 2xot AMGO1_HUMAN + Cell adhesion molecule 2 3m45 CADM2_HUMAN + * Cell adhesion molecule 3 1z9m CADM3_HUMAN + * Cytotoxic and regulatory T-cell molecule 3rbg CRTAM_HUMAN + Poliovirus receptor-related protein 1 3alp PVRL1_HUMAN + Poliovirus receptor-related protein 2 4hza PVRL2_HUMAN + Poliovirus receptor-related protein 4 4frw PVRL4_HUMAN + Neural cell adhesion molecule 1 2vkw NCAM1_HUMAN + Vascular cell adhesion protein 1 1vsc VCAM1_HUMAN + Cadherin-11 2a4c CAD11_HUMAN + Cadherin-1 3q2v CADH1_HUMAN + * Cadherin-20 1zvn CAD20_HUMAN + Cadherin-2 4nup CADH2_HUMAN + Cadherin-3 4nqq CADH3_HUMAN + * Cadherin-5 3ppe CADH5_HUMAN + Cadherin-6 3lnd CADH6_HUMAN + Cadherin-8 1zxk CADH8_HUMAN + Bone marrow stromal antigen 2 ectodomain 2xg7 BST2_HUMAN + * P-selectin 1g1q LYAM3_HUMAN + * Zona pellucida sperm-binding protein 3 3ef7 ZP3_HUMAN + Motility protein B 2zvy MOTB_ECOLI +(no) Cell shape-determining protein MreC 2j5u MREC_ECOLI + Chloroplast translocase 34 3bb1 TOC34_ARATH +(no) Signal recognition particle receptor subunit beta 2ged SRPB_YEAST + Cation-dependent mannose-6-phosphate receptor 2rl8 MPRD_HUMAN + Complement decay-accelerating factor 1ojv MPRD_HUMAN + Cation-independent mannose-6-phosphate receptor 1syo MPRI_HUMAN + Mitochondrial import receptor subunit TOM70 2gw1 TOM70_YEAST + Mitochondrial dynamic protein MID51 4nxt MID51_HUMAN + Putative type II secretion system protein M 1uv7 GSPM_ECOLI + Putative type II secretion system protein G 3fu1 GSPG_ECOLI + t-SNARE affecting a late Golgi compartment protein 1 2c5j TLG1_YEAST +(no) Extended synaptotagmin-2 4p42 ESYT2_HUMAN + Stromal interaction molecule 1 2maj STML1_HUMAN + Calcium uptake protein 1, mitochondrial 4nsd MICU1_HUMAN + Periplasmic domain of TOLR 2jwk TOLR_ECOLI +(no) Lipopolysaccharide export protein LptC 4b54 LPTC_ECOLI + Zinc finger cdgsh-type domain 1 2qh7 CISD1_HUMAN + Fatty aldehyde dehydrogenase 4qgk AL3A2_HUMAN +(no) Mitochondrial Erv2 protein 1jr8 ERV2_YEAST + Sulfhydryl oxidase 1 4p2l QSOX1_HUMAN +(no) Primary amine oxidase 2y73 AOC3_HUMAN + Zinc finger cdgsh-type domain 2 3fnv CISD2_HUMAN +(no) Formate-dependent nitrite reductase subunit NrfG 2e2e NRFG_ECOLI + Polypeptide N-acetylgalactosaminyltransferase 2 4d0t GALT2_HUMAN + N-acetyllactosaminide alpha-1,3-galactosyltransferase 2vfz GGTA1_HUMAN + 3-beta-glucuronosyltransferase 1 1v82 B3GA1_HUMAN + 3-beta-glucuronosyltransferase 2 2d0j B3GA2_HUMAN + 3-beta-glucuronosyltransferase 3 1fgg B3GA3_HUMAN + Beta-1,4-galactosyltransferase 7 4irp B4GT7_HUMAN + UDP-glucuronosyltransferase 2B7 2o6l UD2B7_HUMAN +(no) Beta-1,6-N-acetylglucosaminyltransferase 2gak GCNT1_HUMAN + Catechol o-methyltransferase 4pyq COMT_HUMAN +(no) Catechol o-methyltransferase 2avd CMTD1_HUMAN + Protein-tyrosine sulfotransferase 2 3ap1 TPST2_HUMAN + Adenosine monophosphatase-protein transferase 4u04 FICD_HUMAN + Hexokinase-2 2nzt HXK2_ARATH + Leucyl-cystinyl aminopeptidase 4p8q LCAP_HUMAN + Meprin A subunit beta 4gwm MEP1B_HUMAN + Glutamate carboxypeptidase 2 1z8l FOLH1_HUMAN + Transferrin receptor protein 1 1cx8 TFR1_HUMAN + Dipeptidyl aminopeptidase X. 1xfd DPP6_HUMAN + Dipeptidyl peptidase IV 2qt9 DPP4_HUMAN + * Seprase 1z68 SEPR_HUMAN + Prostatic acid phosphatase 1nd5 PPAP_HUMAN + Ectonucleotide pyrophosphatase/phosphodiesterase 4b56 ENPP1_HUMAN + Calcium-activated nucleotidase 2h2n CANT1_HUMAN +(no) Fatty acid amide hydrolase 1mt5 FAAH1_HUMAN + Bak domain 4u2u BAK_HUMAN + Bcl-2-like protein 1 3inq B2CL1_HUMAN + Bcl-2-like protein 2 2y6w B2CL2_HUMAN + Carbonic anhydrase 12 1jcz CAH12_HUMAN + Carbonic anhydrase 9 3iai CAH9_HUMAN + UDP-glucuronic acid decarboxylase 1 4gll UXS1_HUMAN + Sphingosine-1-phosphate lyase 1 4q6r SGPL1_HUMAN +(no) Prostaglandin E synthase 2 1z9h PGES2_HUMAN + Chloride intracellular channel protein 1 1rk4 CLIC1_HUMAN +(no) * E3 ubiquitin-protein ligase ZNRF3 4c86 ZNRF3_HUMAN +

1 See footnotes for Table 3. “*” indicates that the same protein was already included in Tables 1-3, i.e. its TM domains were experimentally shown to form homodimers. Only one, representative PDB model was included for each dimer. These are all models of homodimeric complexes included in the original release of Membranome database.

Table 5. Bitopic proteins from Membranome that form homodimers according to UniProt annotation.
Family code Protein UniProt code Comment1 Receptor-type tyrosine-protein phosphatase gamma PTPRG_HUMAN + * Receptor-type tyrosine-protein phosphatase H PTPRH_HUMAN + * Receptor-type tyrosine-protein phosphatase epsilon PTPRE_HUMAN + * Erythropoietin receptor EPOR_HUMAN + * Growth hormone receptor GHR_HUMAN + Prolactin receptor PRLR_HUMAN + * Thrombopoietin receptor TPOR_HUMAN + * Granulocyte colony-stimulating factor receptor CSF3R_HUMAN + Interleukin-6 receptor subunit beta IL6RB_HUMAN + * Leptin receptor LEPR_HUMAN + Interleukin-1 receptor accessory protein-like 1 IRPL1_HUMAN + Butyrophilin subfamily 3 member A1 BT3A1_HUMAN + Butyrophilin subfamily 3 member A2 BT3A2_HUMAN +(no) Butyrophilin subfamily 3 member A3 BT3A3_HUMAN + Leukocyte immunoglobulin-like receptor subfamily A member 2 LIRA2_HUMAN + Myelin-oligodendrocyte glycoprotein MOG_HUMAN +(no) Roundabout homolog 1 ROBO1_HUMAN + Natural cytotoxicity triggering receptor 3 NCTR3_HUMAN + T-cell surface glycoprotein CD8 alpha chain CD8A_HUMAN + SLAM family member 5 SLAF5_HUMAN +(no) SLAM family member 6 SLAF6_HUMAN + T-cell-specific surface glycoprotein CD28 CD28_HUMAN + Lymphocyte antigen 6 complex locus protein G6f LY66F_HUMAN + Advanced glycosylation end product-specific receptor RAGE_HUMAN + Signal-regulatory protein beta-1 SIRB1_HUMAN + T-cell immunoreceptor with Ig and ITIM domains TIGIT_HUMAN + Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1 LRIT1_HUMAN +(no) Interleukin-15 receptor subunit alpha I15RA_HUMAN + T-lymphocyte activation antigen CD86 CD86_HUMAN + Cytotoxic T-lymphocyte protein 4 CTLA4_HUMAN + * Inducible T-cell costimulator ICOS_HUMAN + Myotonin-protein kinase DMPK_HUMAN + TGF-beta receptor type-1 TGFR1_HUMAN + TGF-beta receptor type-2 TGFR2_HUMAN - Beta-type platelet-derived growth factor receptor PGFRB_HUMAN + * Mast/stem cell growth factor receptor Kit KIT_HUMAN + * Platelet-derived growth factor receptor alpha PGFRA_HUMAN + * Receptor-type tyrosine-protein kinase FLT3 FLT3_HUMAN + * Vascular endothelial growth factor receptor 1 VGFR1_HUMAN + * Vascular endothelial growth factor receptor 2 VGFR2_HUMAN + * Vascular endothelial growth factor receptor 3 VGFR3_HUMAN + * Epidermal growth factor receptor EGFR_HUMAN + * Receptor tyrosine-protein kinase erbB-2 ERBB2_HUMAN + * Receptor tyrosine-protein kinase erbB-3 ERBB3_HUMAN + * Receptor tyrosine-protein kinase erbB-4 ERBB4_HUMAN + * Ephrin type-A receptor 1 EPHA1_HUMAN + * Fibroblast growth factor receptor 1 FGFR1_HUMAN + * Fibroblast growth factor receptor 2 FGFR2_HUMAN + * Fibroblast growth factor receptor 3 FGFR3_HUMAN + * Fibroblast growth factor receptor 4 FGFR4_HUMAN + * ALK tyrosine kinase receptor ALK_HUMAN + * BDNF/NT-3 growth factors receptor NTRK2_HUMAN + * Epithelial discoidin domain-containing receptor 1 DDR1_HUMAN + * High affinity nerve growth factor receptor NTRK1_HUMAN + * Leukocyte tyrosine kinase receptor LTK_HUMAN + * Tyrosine-protein kinase transmembrane receptor ROR2 ROR2_HUMAN +(no) * Angiopoietin-1 receptor TIE2_HUMAN + * Tyrosine-protein kinase receptor TYRO3 TYRO3_HUMAN + * AarF domain-containing protein kinase 4 ADCK4_HUMAN + * Atypical kinase ADCK3, mitochondrial ADCK3_HUMAN + * LRR receptor-like serine/threonine-protein kinase ERECTA ERECT_ARATH + LRR receptor-like serine/threonine-protein kinase ERL1 ERL1_ARATH + LRR receptor-like serine/threonine-protein kinase FLS2 FLS2_ARATH + Protein BRASSINOSTEROID INSENSITIVE 1 BRI1_ARATH + Somatic embryogenesis receptor kinase 1 SERK1_ARATH + Somatic embryogenesis receptor kinase 2 SERK2_ARATH + Serine/threonine-protein kinase/endoribonuclease IRE1a IRE1A_ARATH + Serine/threonine-protein kinase/endoribonuclease IRE1 ERN1_HUMAN + * Serine/threonine-protein kinase/endoribonuclease IRE1 IRE1_YEAST + Putative serine/threonine-protein kinase-like protein CCR3 ACCR3_ARATH + Serine/threonine-protein kinase-like protein ACR4 ACR4L_ARATH + * Serine/threonine-protein kinase-like protein CCR1 ACCR1_ARATH + Serine/threonine-protein kinase-like protein CCR2 ACCR2_ARATH + Serine/threonine-protein kinase-like protein CCR4 ACCR4_ARATH + Chitin elicitor receptor kinase 1 CERK1_ARATH + Muscle, skeletal receptor tyrosine protein kinase MUSK_HUMAN + * Atrial natriuretic peptide receptor 3 ANPRC_HUMAN + Atrial natriuretic peptide receptor A ANPRA_HUMAN + * B-cell differentiation antigen CD72 CD72_HUMAN + C-type lectin domain family 12 member B CL12B_HUMAN + C-type lectin domain family 1 member B CLC1B_HUMAN + C-type lectin domain family 2 member A CLC2A_HUMAN + C-type lectin domain family 2 member D CLC2D_HUMAN + C-type lectin domain family 4 member E CLC4E_HUMAN + C-type lectin domain family 5 member A CLC5A_HUMAN + C-type lectin domain family 7 member A CLC7A_HUMAN + C-type lectin domain family 9 member A CLC9A_HUMAN + Early activation antigen CD69 CD69_HUMAN + Killer cell lectin-like receptor subfamily B member 1 KLRB1_HUMAN + Killer cell lectin-like receptor subfamily F member 1 KLRF1_HUMAN + Killer cell lectin-like receptor subfamily F member 2 KLRF2_HUMAN + Killer cell lectin-like receptor subfamily G member 1 KLRG1_HUMAN + NKG2-D type II integral membrane protein NKG2D_HUMAN + Oxidized low-density lipoprotein receptor 1 OLR1_HUMAN + Low-density lipoprotein receptor-related protein 5 LRP5_HUMAN + Low-density lipoprotein receptor-related protein 6 LRP6_HUMAN + Tumor necrosis factor receptor superfamily member 3 TNR3_HUMAN + Tumor necrosis factor receptor superfamily member 5 TNR5_HUMAN + Tumor necrosis factor receptor superfamily member 10B TR10B_HUMAN + Tumor necrosis factor receptor superfamily member 16 TNR16_HUMAN + * Tumor necrosis factor receptor superfamily member 25 TNR25_HUMAN + CD27 antigen CD27_HUMAN + Toll-like receptor 10 TLR10_HUMAN + * Toll-like receptor 3 TLR3_HUMAN + * Toll-like receptor 4 TLR4_HUMAN + * Toll-like receptor 5 TLR5_HUMAN + * Toll-like receptor 8 TLR8_HUMAN + * Interleukin-17 receptor D I17RD_HUMAN + T-cell surface glycoprotein CD3 zeta chain CD3Z_HUMAN + * Integrin alpha-4 ITA4_HUMAN + * Integrin beta-1 ITB1_HUMAN +(no) * Neuropilin-1 NRP1_HUMAN + * Plexin-A2 PLXA2_HUMAN + * Plexin-B3 PLXB3_HUMAN + Plexin-C1 PLXC1_HUMAN + Syndecan-4 SDC4_HUMAN + * Sialomucin core protein 24 MUC24_HUMAN + Amyloid beta A4 protein A4_HUMAN + * Amyloid-like protein 1 APLP1_HUMAN + Lymphatic vessel endothelial hyaluronic acid receptor 1 LYVE1_HUMAN + HLA class I histocompatibility antigen, alpha chain G HLAG_HUMAN + T-lymphocyte activation antigen CD80 CD80_HUMAN +(no) Semaphorin-4D SEM4D_HUMAN + Semaphorin-6A SEM6A_HUMAN + Neuroligin-3 NLGN3_HUMAN + Neuroligin-4, X-linked NLGNX_HUMAN + Neuroligin-4, Y-linked NLGNY_HUMAN + Fms-related tyrosine kinase 3 ligand FLT3L_HUMAN + Kit ligand SCF_HUMAN + * Tumor necrosis factor ligand superfamily member 18 TNF18_HUMAN +(no) Protein APCDD1 APCD1_HUMAN + Macrophage colony-stimulating factor 1 CSF1_HUMAN + TYRO protein tyrosine kinase-binding protein TYOBP_HUMAN + * LINGO-1 protein LIGO1_HUMAN + Hematopoietic cell signal transducer HCST_HUMAN + Melanocortin-2 receptor accessory protein 2 MRAP2_HUMAN + Melanocortin-2 receptor accessory protein MRAP_HUMAN + Signaling threshold-regulating transmembrane adapter 1 SIT1_HUMAN + T-cell receptor-associated transmembrane adapter 1 TRAT1_HUMAN + Coxsackievirus and adenovirus receptor CXAR_HUMAN + * Hepatocyte cell adhesion molecule HECAM_HUMAN + Junctional adhesion molecule-like JAML1_HUMAN + Myelin protein P0 MYP0_HUMAN + * Neurofascin NFASC_HUMAN + Kin of IRRE-like protein 1 KIRR1_HUMAN + Amphoterin-induced protein 1 AMGO1_HUMAN + Intercellular adhesion molecule 1 ICAM1_HUMAN + Cell adhesion molecule 1 CADM1_HUMAN + Cell adhesion molecule 2 CADM2_HUMAN + * Cell adhesion molecule 3 CADM3_HUMAN + * Cell adhesion molecule 4 CADM4_HUMAN + Poliovirus receptor-related protein 1 PVRL1_HUMAN + Poliovirus receptor-related protein 3 PVRL3_HUMAN + T-cell surface protein tactile TACT_HUMAN + Mucosal addressin cell adhesion molecule 1 MADCA_HUMAN + Mucin-13 MUC13_HUMAN + Cadherin-1 CADH1_HUMAN + * Protocadherin Fat 2 FAT2_HUMAN + Glycophorin-A GLPA_HUMAN + * Bone marrow stromal antigen 2 BST2_HUMAN + * Teneurin-1 TEN1_HUMAN + Teneurin-2 TEN2_HUMAN + Teneurin-3 TEN3_HUMAN + Teneurin-4 TEN4_HUMAN + P-selectin glycoprotein ligand 1 SELPL_HUMAN + Sarcolemmal membrane-associated protein SLMAP_HUMAN + Podocalyxin-like protein 2 PDXL2_HUMAN + Izumo sperm-egg fusion protein 1 IZUM1_HUMAN + Izumo sperm-egg fusion protein 3 IZUM3_HUMAN + Endoglin EGLN_HUMAN + Zona pellucida sperm-binding protein 1 ZP1_HUMAN + Zona pellucida sperm-binding protein 2 ZP2_HUMAN + Zona pellucida sperm-binding protein 3 ZP3_HUMAN + Collagen alpha-1(XXV) chain COPA1_HUMAN + SUN domain-containing protein 1 SUN1_DICDI - WPP domain-interacting protein 1 WIP1_ARATH + WPP domain-interacting protein 2 WIP2_ARATH + WPP domain-interacting tail-anchored protein 1 WIT1_ARATH +(no) Cell division protein FtsL FTSL_ECOLI + * Cell shape-determining protein MreC MREC_ECOLI + Mitochondrial import inner membrane translocase subunit TIM14 TIM14_YEAST + DnaJ-like protein DjlA DJLA_ECOLI + * Translocase of chloroplast 120, chloroplastic TC120_ARATH +(no) Translocase of chloroplast 132, chloroplastic TC132_ARATH + Translocase of chloroplast 159, chloroplastic TC159_ARATH + Translocase of chloroplast 90, chloroplastic TOC90_ARATH +(no) Translocase of chloroplast 34, chloroplastic TOC34_ARATH +(no) Leucine-rich repeat-containing protein 59 LRC59_HUMAN + Protein RIC-3 RIC3_HUMAN +(no) Cation-dependent mannose-6-phosphate receptor MPRD_HUMAN + Integral membrane protein 2B ITM2B_HUMAN + Stomatin-like protein 3 STML3_HUMAN +(no) Protein SCO1 homolog, mitochondrial SCO1_HUMAN + ATPase family AAA domain-containing protein 3A ATD3A_HUMAN +(no) BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 BNIP3_HUMAN + * BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like BNI3L_HUMAN + Mitochondrial dynamic protein MID51 MID51_HUMAN + Synaptotagmin-10 SYT10_HUMAN + Synaptotagmin-11 SYT11_HUMAN +(no) Synaptotagmin-12 SYT12_HUMAN +(no) Synaptotagmin-14 SYT14_HUMAN + Synaptotagmin-15 SYT15_HUMAN + Synaptotagmin-3 SYT3_HUMAN +(no) Synaptotagmin-5 SYT5_HUMAN + Synaptotagmin-6 SYT6_HUMAN + Synaptotagmin-8 SYT8_HUMAN +(no) Extended synaptotagmin-2 ESYT2_HUMAN + Transmembrane emp24 domain-containing protein 10 TMEDA_HUMAN + Transmembrane emp24 domain-containing protein 1 TMED1_HUMAN + Transmembrane emp24 domain-containing protein 2 TMED2_HUMAN + Transmembrane emp24 domain-containing protein 7 TMED7_HUMAN +(no) Transmembrane emp24 domain-containing protein 9 TMED9_HUMAN + Golgin subfamily A member 5 GOGA5_HUMAN + Golgin subfamily B member 1 GOGB1_HUMAN + Protein CASP CASP_HUMAN + Vesicle-associated membrane protein-associated protein A VAPA_HUMAN + Vesicle-associated membrane protein-associated protein B/C VAPB_HUMAN + Vesicle-associated protein 1-1 VAP11_ARATH + Kinectin KTN1_HUMAN + Plasmalemma vesicle-associated protein PLVAP_HUMAN + Dyslexia-associated protein KIAA0319 K0319_HUMAN + Mitochondrial fission factor MFF_HUMAN + Plasma membrane ATPase proteolipid 1 PMP1_YEAST + Plasma membrane ATPase proteolipid 2 PMP2_YEAST + Multidrug resistance protein A EMRA_ECOLI + Lipopolysaccharide export system protein LptC LPTC_ECOLI + Cyclic AMP-responsive element-binding protein 3 CREB3_HUMAN + Cyclic AMP-responsive element-binding protein 3-like protein 3 CR3l3_HUMAN + bZIP transcription factor 28 BZP28_ARATH + Cyclic AMP-dependent transcription factor ATF-6 alpha ATF6A_HUMAN + Cyclic AMP-dependent transcription factor ATF-6 beta ATF6B_HUMAN + Amine oxidase [flavin-containing] A AOFA_HUMAN + Amine oxidase [flavin-containing] B AOFB_HUMAN + CDGSH iron-sulfur domain-containing protein 1 CISD1_HUMAN + CDGSH iron-sulfur domain-containing protein 2 CISD2_HUMAN +(no) Vitamin D 25-hydroxylase CP2R1_HUMAN +(no) Corticosteroid 11-beta-dehydrogenase isozyme 1 DHI1_HUMAN + Aldehyde dehydrogenase family 3 member I1, chloroplastic AL3I1_ARATH + FAD-linked sulfhydryl oxidase ERV2 ERV2_YEAST + Type III iodothyronine deiodinase IOD3_HUMAN + Transmembrane prolyl 4-hydroxylase P4HTM_HUMAN + Membrane primary amine oxidase AOC3_HUMAN + Beta-1,4 N-acetylgalactosaminyltransferase 1 B4GN1_HUMAN + Xyloside xylosyltransferase 1 XXLT1_HUMAN Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 B3GA1_HUMAN + Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 B3GA2_HUMAN + Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 B3GA3_HUMAN + Beta-1,4-galactosyltransferase 1 B4GT1_HUMAN + Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 C1GLT_HUMAN + Chitobiosyldiphosphodolichol beta-mannosyltransferase ALG1_YEAST + Probable arabinosyltransferase ARAD1 ARAD1_ARATH +(no) Probable arabinosyltransferase ARAD2 ARAD2_ARATH + Fukutin-related protein FKRP_HUMAN + Catechol O-methyltransferase domain-containing protein 1 CMTD1_HUMAN + Carbohydrate sulfotransferase 15 CHSTF_HUMAN + Carbohydrate sulfotransferase 2 CHST2_HUMAN + Protein-tyrosine sulfotransferase 2 TPST2_HUMAN + Penicillin-binding protein 1B PBPB_ECOLI + Retroviral-like aspartic protease 1 APRV1_HUMAN + Aminopeptidase N AMPN_HUMAN + Aminopeptidase Q AMPQ_HUMAN + Glutamyl aminopeptidase AMPE_HUMAN + Leucyl-cystinyl aminopeptidase LCAP_HUMAN + Thyrotropin-releasing hormone-degrading ectoenzyme TRHDE_HUMAN + Collectrin TMM27_HUMAN +(no) Meprin A subunit alpha MEP1A_HUMAN + Endothelin-converting enzyme 1 ECE1_HUMAN + Glutamate carboxypeptidase 2 FOLH1_HUMAN + N-acetylated-alpha-linked acidic dipeptidase 2 NALD2_HUMAN + Transferrin receptor protein 1 TFR1_HUMAN + Transferrin receptor protein 2 TFR2_HUMAN + Dipeptidyl aminopeptidase-like protein 6 DPP6_HUMAN + Dipeptidyl peptidase 4 DPP4_HUMAN + * Seprase SEPR_HUMAN + Mitochondrial cardiolipin hydrolase PLD6_HUMAN + Prostatic acid phosphatase, isoform 2 PPAP_HUMAN + Testicular acid phosphatase PPAT_HUMAN + Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 ENPP1_HUMAN + Guanosine-diphosphatase GDA1_YEAST + N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase NAGPA_HUMAN + Klotho KLOT_HUMAN + Alpha-mannosidase 2 GMAN2_ARATH + Alpha-mannosidase 2 MA2A1_HUMAN + Alpha-mannosidase 2x MA2A2_HUMAN +(no) Fatty-acid amide hydrolase 1 FAAH1_HUMAN + Fatty-acid amide hydrolase 2 FAAH2_HUMAN +(no) Probable inactive purple acid phosphatase 2 PPA2_ARATH + Probable inactive purple acid phosphatase 9 PPA9_ARATH + AMP deaminase AMPD_ARATH + Complement decay-accelerating factor DAF_HUMAN + Apoptosis regulator BAX BAX_HUMAN + * Apoptosis regulator Bcl-2 BCL2_HUMAN +(no) Bcl-2 homologous antagonist/killer BAK_HUMAN + Bcl-2-like protein 1 B2CL1_HUMAN + Receptor-binding cancer antigen expressed on SiSo cells RCAS1_HUMAN +(no) Carbonic anhydrase 12 CAH12_HUMAN + UDP-glucuronic acid decarboxylase 2 UXS2_ARATH + Sphingosine-1-phosphate lyase 1 SGPL1_HUMAN +(no) Prostaglandin E synthase 2 PGES2_HUMAN + Chloride intracellular channel protein 1 CLIC1_HUMAN +(no) * Peptidyl-prolyl cis-trans isomerase D PPID_ECOLI + Long-chain fatty acid transport protein 1 S27A1_HUMAN + Cell cycle exit and neuronal differentiation protein 1 CEND_HUMAN +

See footnotes for Table 4.

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