Supplementary Table S1: All THD/C1q and CRD Structures Deposited in the PDB

Supplementary Table S1: All THD/C1q and CRD Structures Deposited in the PDB

NAMES / STRUCTURAL DETAILS
NAME / HGNC / PROTEIN / Nb / RMSD Å / PDB / Res. / Species / Chain / Cov. / Cplx
Human TNFL members (with or without available structures)
TNF1 / LTA / LT-α / 1 / n.a. / 1TNR / 2.85 / H. sapiens / A / yes / yes
TNF2 / TNF / TNF-α / 13 / 0.542 / 1A8M / 2.3 / H. sapiens / A-C / yes / no
1TNF / 2.60 / H. sapiens / A-C / yes / no
2AZ5 / 2.10 / H. sapiens / A-D / no / no
2E7A / 1.80 / H. sapiens / A-C / A / no
2TNF / 1.40 / M. musculus / A-C / no / no
2TUN / 3.10 / H. sapiens / A-F / yes / no
2ZJC / 2.50 / H. sapiens / A-C / C / no
2ZPX / 2.83 / H. sapiens / A-C / no / no
3ALQ / 3.00 / H. sapiens / A-F / no / yes
3IT8 / 2.80 / H. sapiens / A-C/G-I / yes / no
3L9J / 2.10 / H. sapiens / T / yes / no
4TSV / 1.80 / H. sapiens / A / yes / no
5TSW / 2.50 / H. sapiens / A-F / yes / no
TNF3 / LTB / LT-β / no available structure
TNF4 / TNFSF4 / OX40L / 3 / 0.911 / 2HEV / 2.41 / H. sapiens / F / yes / yes
2HEW / 1.45 / M. musculus / F / yes / no
2HEY / 2.00 / M. musculus / F-G / yes / yes
TNF5 / CD40LG / CD40L / 4 / 0.409 / 1ALY / 2.00 / H. sapiens / A / yes / no
1I9R / 3.10 / H. sapiens / A-C / yes / no
3LKJ / 2.50 / H. sapiens / A-C / no / no
3QD6 / 3.50 / H. sapiens / A-F / no / yes
TNF6 / FASLG / FASL / no available structure
TNF7 / CD70 / CD70L / no available structure
TNF8 / TNFSF8 / CD30L / no available structure
TNF9 / TNFSF9 / 4-1BBL / 1 / n.a. / 2X29 / 2.30 / H. sapiens / A / no / no
TNF10 / TNFSF10 / TRAIL / 5 / 0.218 / 1D0G / 2.40 / H. sapiens / A/B/D / no / yes
1D2Q / 2.80 / H. sapiens / A-B / no / no
1D4V / 2.20 / H. sapiens / B / yes / yes
1DG6 / 1.30 / H. sapiens / A / no / no
1DU3 / 2.20 / H. sapiens / D-F/J-L / no / yes
TNF11 / TNFSF11 / RANKL / 5 / 0.215 / 1IQA / 2.20 / M. musculus / A-C / yes / no
1JTZ / 2.60 / M. musculus / X-Z / yes / no
1S55 / 1.90 / M. musculus / A-C / yes / no
3ME2 / 2.80 / M. musculus / A / yes / yes
3QBQ / 2.50 / M. musculus / A/C / yes / yes
TNF12 / TNFSF12 / TWEAK / no available structure
TNF13 / TNFSF13 / APRIL / 6 / 0.228 / 1U5X / 1.80 / M. musculus / A / no / yes
1U5Y / 2.30 / M. musculus / A/B/D / A/B / no
1U5Z / 2.40 / M. musculus / A / no / no
1XU1 / 1.90 / M. musculus / A/B/D / yes / yes
1XU2 / 2.35 / M. musculus / A/B/D / yes / yes
3K48 / 2.80 / M. musculus / A/B/D / yes / no
TNF13B / TNFSF13B / BAFF / 7 / 0.206 / 1JH5 / 3.00 / H. sapiens / A-J / yes / no
1KD7 / 2.80 / H. sapiens / A-C/K-M / yes / no
1KXG / 2.00 / H. sapiens / A-F / yes / no
1OQD / 2.60 / H. sapiens / A-J / yes / yes
1OQE / 2.50 / H. sapiens / A-J / yes / yes
1OSG / 3.00 / H. sapiens / A-F / yes / yes
1OTZ / 3.30 / H. sapiens / 0-x / yes / no
TNF14 / TNFSF14 / LIGHT / 1 / n.a. / 3UGN / 2.59 / H. sapiens / A-C / no / no
TNF15 / TNFSF15 / VEGI / 7 / 0.217 / 2O0O / 3.00 / H. sapiens / A-C / no / no
2QE3 / 2.50 / H. sapiens / A / no / no
2RE9 / 2.10 / H. sapiens / A-C / yes / no
2RJK / 2.30 / H. sapiens / A / no / no
2RJL / 2.05 / H. sapiens / A / no / no
3K51 / 2.45 / H. sapiens / A / no / yes
3MI8 / 2.95 / H. sapiens / A / no / yes
TNF18 / TNFSF18 / GITRL / 9 / 0.757 / 2Q1M / 2.30 / H. sapiens / A / yes / no
2Q8O / 1.75 / M. musculus / A/B / no / no
2QDN / 2.09 / M. musculus / A/B / no / no
2R30 / 3.20 / H. sapiens / A / yes / no
2R32 / 1.95 / H. sapiens / A / no / no
3B93 / 2.20 / H. sapiens / A-C / A / no
3B94 / 2.50 / H. sapiens / A-D / no / no
3B9I / 2.49 / M. musculus / A/B / yes / no
3FC0 / 1.76 / M. musculus / A/B / A / no
EDA-A1 / EDA / EDA var. 1 / 1 / n.a / 1RJ7 / 2.30 / H. sapiens / A / yes / no
EDA-A2 / EDA / EDA var.2 / 1 / n.a / 1RJ8 / 2.20 / H. sapiens / A / yes / no
C1QL members (with available structure only)
ADIPO / ADIPOQ / ACRP30 / 3 / 0.529 / 4DOU / 2.00 / H. sapiens / A / no / no
1C3H / 2.10 / M. musculus / A-F / yes / no
1C28 / 2.10 / M. musculus / A-C / no / no
C1QA / C1QA / C1q A / 5 / 0.184 / 1PK6 / 1.85 / H. sapiens / A / yes / no
2JG8 / 2.05 / H. sapiens / A/D / yes / no
2JG9 / 1.90 / H. sapiens / A/D / yes / no
2WNU / 2.30 / H. sapiens / A/D / yes / no
2WNV / 1.25 / H. sapiens / A/D / no / no
C1QB / C1QB / C1q B / 5 / 0.184 / 1PK6 / 1.85 / H. sapiens / B / yes / no
2JG8 / 2.05 / H. sapiens / B/E / yes / no
2JG9 / 1.90 / H. sapiens / B/E / yes / no
2WNU / 2.30 / H. sapiens / B/E / yes / no
2WNV / 1.25 / H. sapiens / B/E / no / no
C1QC / C1QC / C1q C / 5 / 0.184 / 1PK6 / 1.85 / H. sapiens / C / yes / no
2JG8 / 2.05 / H. sapiens / C/F / yes / no
2JG9 / 1.90 / H. sapiens / C/F / yes / no
2WNU / 2.30 / H. sapiens / C/F / yes / no
2WNV / 1.25 / H. sapiens / C/F / yes / no
CO8A1 / COL8A1 / Collagen α-1 VIII / 1 / n.a. / 1O91 / 1.85 / M. musculus / A / yes / no
COAA1 / COL10A1 / Collagen α-1 X / 1 / n.a. / 1GR3 / 2.00 / H. sapiens / A / yes / no
EMIL1 / EMILIN1 / Emilin 1 / 2 / 0.310 / 2KA3 / NMR / H. sapiens / A-C / no / no
2OII / NMR / H. sapiens / A-C / no / no
Human TNFR members (with or without available structure)
TNFR1 / TNFRSF1A / TNFR-R1 / 4 / 0.578 / 1EXT / 1.85 / H. sapiens / A/B / 1-2-3-4 / no
1FT4 / 2.90 / H. sapiens / A/B / 1-2-3 / no
1NCF / 2.25 / H. sapiens / A/B / 1-2-3 / no
1TNR / 2.85 / H. sapiens / R / 1-2-3 / yes
TNFR2 / TNFRSF1B / TNFR-R2 / 1 / n.a. / 3ALQ / 3.00 / H. sapiens / R / 1-2-3-4 / yes
TNFR3 / LTBR / LTβ-R / no available structure
TNFR4 / TNFRSF4 / OX40 / 2 / 0.334 / 2HEV / 2.41 / H. sapiens / R / 1-2-3-4 / no
2HEY / 2.00 / H. sapiens / R/T / R: 1-2-3-4 / yes
TNFR5 / CD40 / CD40 / 1 / n.a. / 3QD6 / 3.50 / H. sapiens / R-U / yes
TNFR6 / FAS / FAS / no available structure
TNFR6B / TNFRSF6B / DcR3 / 3 / 0.514 / 3K51 / 2.45 / H. sapiens / B / 1-2-3-4 / yes
3MHD / 2.90 / H. sapiens / D / 1-2-3 / no
3MI8 / 2.95 / H. sapiens / D / 1-2 / yes
TNFR7 / CD27 / CD27 / no available structure
TNFR8 / TNFRSF8 / CD30 / no available structure
TNFR9 / TNFRSF9 / 4-1BB / no available structure
TNFR10A / TNFRSF10A / DR4 / no available structure
TNFR10B / TNFRSF10B / DR5 / 5 / 0.393 / 1D0G / 2.40 / H. sapiens / R-T / 1-2-3 / yes
1D4V / 2.20 / H. sapiens / A / 1-2-3 / yes
1DU3 / 2.20 / H. sapiens / A-C/G-I / B/G: 1-2-3 / yes
1ZA3 / 3.35 / H. sapiens / R/S / S 1-2-3 / no
2H9G / 2.32 / H. sapiens / R/S / R 1-2-3 / no
TNFR10C / TNFRSF10C / DcR1 / no available structure
TNFR10D / TNFRSF10D / DcR2 / no available structure
TNFR11A / TNFRSF11A / RANK / 3 / 0.525 / 3ME2 / 2.80 / M. musculus / R / 1-2-3-4 / yes
3ME4 / 2.01 / M. musculus / A / A: 1-2-3-4 / yes
3QBQ / 2.50 / M. musculus / B/D / 1-2-3-4 / yes
TNFR11B / TNFRSF11B / OPG / no available structure
TNFR12 / TNFRSF12A / TWEAK-R / 3 / 0.997 / 2EQP / NMR / H. sapiens / A / no S-S / no
2KMZ / NMR / H. sapiens / A / 1 / no
2RPJ / NMR / H. sapiens / A / 1 / no
TNFR13B / TNFSF13B / TACI / 2 / 0.750 / 1XU1 / 1.90 / H. sapiens / R-T / 1 / yes
1XUT / NMR / H. sapiens / A / 1
TNFR13C / TNFRSF13C / BAFF-R / 5 / 0.459 / 1MPV / NMR / H. sapiens / A / 1
1OQE / 2.50 / H. sapiens / K-R / 1 / yes
1OSX / NMR / H. sapiens / A / no
1P0T / 3.30 / H. sapiens / 0-x / 1
2HFG / 2.61 / H. sapiens / R / 1
TNFR14 / TNFRSF14 / HVEM / 2 / 0.663 / 1JMA / 2.65 / H. sapiens / B / 1-2 / no
2AW2 / 2.80 / H. sapiens / B/Y / 1-2 / no
TNFR16 / NGFR / NGFR / 3 / 0.521 / 1SG1 / 2.40 / R. norvegicus / X / 1-2-3-4 / n.a.
3IJ2 / 3.75 / R. norvegicus / X/Y / 1-2-3-4
3BUK / 2.60 / R. norvegicus / C/D / (1)-2-3-4
TNFR17 / TNFRSF17 / BCMA / 3 / 0.947 / 1XU2 / 2.35 / H. sapiens / R-T / 1 / yes
1OQD / 2.60 / H. sapiens / K-R / 1 (except N) / yes
2KN1 / NMR / H. sapiens / A / 1 / no
TNFR18 / TNFRSF18 / GITR / no available structure
TNFR19 / TNFRSF19 / TROY / no available structure
TNFR19L / TNFRSF19L / RELT / no available structure
TNFR21 / TNFRSF21 / DR6 / 1 / n.a. / 3QO4 / 2.20 / H. sapiens / A / 1-2-3-4 / no
TNFR25 / TNFRSF25 / DR3 / no available structure
XEDAR / EDA2R / XEDAR / no available structure
EDAR / EDAR / EDAR / no available structure
Other TNFR members (with structure only)
CRME / CRME / CRME / 1 / n.a. / 2UWI / 2.00 / V. virus / A / 1-2-3 / no

Supplementary Table S1: All THD/C1q and CRD structures deposited in the PDB.

PDB / THD / Large / Small / Others
With 3D structure / TNF1 / 4.4e-08 / n.a.
TNF2 / 2.2e-11 / n.a.
TNF5 / 1.5e-07 / n.a.
TNF10 / 5e-14 / 2.0e-05
TNF11 / 3.2e-08 / n.a.
TNF15 / 6.2e-10 / n.a.
TNF13 / 2.8e-10 / n.a.
TNF13B / 7.4e-13 / n.a.
EDA-A1 / 6.4e-11 / n.a.
EDA-A2 / 7.3e-12 / n.a.
TNF4 / 3.1e-05 / n.a.
TNF18 / 6.6e-07 / 8.1e-06
Without 3D structure / TNF3 / 1.9e-22 / 9.2e-05 / n.a.
TNF6 / 2.0e-32 / 6.7e-10 / n.a.
TNF7 / 4.4e-08 / n.a. / n.a.
TNF8 / 8.3e-08 / n.a. / n.a.
TNF9 / 2.3e-05 / n.a. / n.a.
TNF12 / 1.2e-09 / 7.0e-06 / n.a.
TNF14 / 5.8e-29 / 7.1e-08 / n.a.

Supplementary Table S2: human THDs annotation using HMM profiles derived from the THDs T-RMSD structure-based classification (Blue: L-THD. Green: S-THD. Grey: V-THD).

Location / Small TNFR / N terminal / CRD2 / CRD3 / CRD4 / >CRD4 / Core
Type S / 5 (100%) / 0 / 0 / 0 / 1 (7%) / 0 / 1 (1.5%)
Type L-1 / 0 / 15 (60%) / 0 / 0 / 0 / 0 / 0
Type L-2 / 0 / 0 / 21 (84 %) / 0 / 0 / 1 (50%) / 22 (33%)
Type L-3 / 0 / 0 / 0 / 16 (64%) / 0 / 0 / 16 (24%)
Type L-4 / 0 / 0 / 3 (12%) / 1 (4%) / 10 (71.5%) / 0 / 14 (21%)
Undetermined / 0 / 10 (40%) / 1 (4%) / 8 (32%) / 3 (21.5%) / 1 (50%) / 13 (19.5%)
Type L (2-3-4) / 0 / 0 / 24 (96%) / 17 (68%) / 10 (71.5%) / 1 (50%) / 52 (78%)
Total / 5 / 25 / 25 / 25 / 14 / 2 / 66

Supplementary Table S3: Correspondence between CRD position within the TNFR architecture and CRD Type as defined in this work.