SMTL ID : 8dvd.1

Cryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with human bNAb PGT145

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

18 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 2 residues within 4Å: Chain A: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain A: N.108, N.109 Ligands: NAG-NAG.32, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 2 residues within 4Å: Chain B: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 3 residues within 4Å: Chain C: N.100, S.102, L.103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 3 residues within 4Å: Chain D: E.173, N.190, T.191 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 3 residues within 4Å: Chain D: N.222, K.235, V.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 2 residues within 4Å: Chain D: Q.132, N.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.25: 2 residues within 4Å: Chain D: N.294, T.296 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 6 residues within 4Å: Chain A: F.121 Chain E: N.15, N.57, R.271 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN-MAN-MAN.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.35: 2 residues within 4Å: Chain E: N.190, T.191 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.36: 4 residues within 4Å: Chain E: E.44, N.222, K.235, V.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.43: 1 residues within 4Å: Chain E: N.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.50: 1 residues within 4Å: Chain E: N.294 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.52: 4 residues within 4Å: Chain F: N.15, N.57 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.65, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.56: 2 residues within 4Å: Chain F: Q.174, N.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.57: 3 residues within 4Å: Chain F: N.222, K.235, V.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.64: 3 residues within 4Å: Chain F: Q.132, N.134, T.136 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.71: 4 residues within 4Å: Chain F: T.357, A.358, Q.455, N.457 No protein-ligand interaction detected (PLIP)

15 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: L.122, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain B: L.122, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain C: L.122, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain D: N.57, R.271 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain D: G.179, N.180 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 5 residues within 4Å: Chain D: N.262, N.280, Y.282, Y.283, E.334 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 2 residues within 4Å: Chain D: N.124, T.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 4 residues within 4Å: Chain D: D.449, W.450, I.451, N.457 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain D: E.160, N.162, N.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 2 residues within 4Å: Chain E: N.124, T.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 5 residues within 4Å: Chain E: K.147, E.160, Y.161, N.162, N.314 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.314 NAG-NAG-BMA.51: 2 residues within 4Å: Chain E: I.451, N.457 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.62: 3 residues within 4Å: Chain F: M.122, N.124, T.126 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.67: 3 residues within 4Å: Chain F: E.160, N.162, N.314 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.314 NAG-NAG-BMA.72: 2 residues within 4Å: Chain F: N.294, T.296 No protein-ligand interaction detected (PLIP)

16 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain B: N.109 Ligands: NAG-NAG.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 3 residues within 4Å: Chain C: N.109 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 4 residues within 4Å: Chain D: N.92, S.94, E.95, R.98 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 6 residues within 4Å: Chain D: I.130, A.131, T.436, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.21 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.130, D:A.131 NAG-NAG-BMA-MAN-MAN.19: 3 residues within 4Å: Chain D: Y.282, N.284, K.327 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.28: 7 residues within 4Å: Chain D: G.270, R.271, D.272, N.273, R.344, W.450, I.451 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.33: 3 residues within 4Å: Chain E: N.92, E.95, R.98 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 6 residues within 4Å: Chain E: I.130, A.131, T.436, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.42, NAG-NAG-BMA-MAN-MAN-MAN-MAN.42 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.130, E:A.131 NAG-NAG-BMA-MAN-MAN.40: 3 residues within 4Å: Chain E: Y.282, N.284, K.327 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.45: 4 residues within 4Å: Chain E: R.90, N.149, T.158 Chain G: Y.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.49: 7 residues within 4Å: Chain E: G.270, R.271, D.272, N.273, W.450, I.451 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.54: 2 residues within 4Å: Chain F: N.92, E.95 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.58: 8 residues within 4Å: Chain F: I.130, A.131, K.288, R.374, T.436, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.63, NAG-NAG-BMA-MAN-MAN-MAN-MAN.63 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.130 NAG-NAG-BMA-MAN-MAN.61: 2 residues within 4Å: Chain F: Y.282, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.66: 3 residues within 4Å: Chain F: R.90, N.149, T.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.70: 7 residues within 4Å: Chain F: G.270, R.271, D.272, N.273, T.346, W.450, I.451 No protein-ligand interaction detected (PLIP)

11 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.11: 3 residues within 4Å: Chain C: G.15 Chain D: N.48 Ligands: NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain D: N.176, T.178 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.178 Hydrogen bonds: D:T.178 NAG-NAG.27: 1 residues within 4Å: Chain D: N.349 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain A: G.15 Chain E: N.48 Ligands: NAG-NAG-BMA-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain E: G.179, N.180 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 1 residues within 4Å: Chain E: N.176 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 1 residues within 4Å: Chain E: N.349 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 2 residues within 4Å: Chain F: N.48 Ligands: NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 2 residues within 4Å: Chain F: G.179, N.180 No protein-ligand interaction detected (PLIP) NAG-NAG.68: 1 residues within 4Å: Chain F: N.176 No protein-ligand interaction detected (PLIP) NAG-NAG.69: 1 residues within 4Å: Chain F: N.349 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.17: 6 residues within 4Å: Chain D: D.352, N.355, E.390, D.391, R.392, N.393 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.393 NAG-NAG-BMA-MAN-MAN-MAN.38: 7 residues within 4Å: Chain E: K.119, D.352, I.354, N.355, E.390, R.392, N.393 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.59: 6 residues within 4Å: Chain F: K.336, D.352, N.355, E.390, R.392, N.393 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.21: 12 residues within 4Å: Chain D: K.200, W.203, D.204, A.205, N.256, N.372, C.373, R.431, T.436, N.438, S.439 Ligands: NAG-NAG-BMA-MAN-MAN.16 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.438 Hydrogen bonds: D:D.204, D:A.205, D:N.438

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23: 9 residues within 4Å: Chain D: N.15, S.52, F.53, D.54, G.270, R.344, K.476 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.54 Hydrogen bonds: D:D.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.24: 14 residues within 4Å: Chain D: N.149, T.158 Chain G: N.31, H.32, H.53, S.100, K.101, H.102, R.103, L.104, R.105 Chain H: T.33, G.34, A.35 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:K.101, G:H.102, G:R.103, G:R.103, H:G.34, H:A.35 Hydrophobic interactions: G:L.104 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.65: 10 residues within 4Å: Chain F: N.15, S.52, F.53, D.54, F.229, G.270, R.344, K.476 Ligands: NAG-NAG-BMA-MAN.52, NAG-NAG-BMA-MAN.52 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.54

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.39: 6 residues within 4Å: Chain E: N.262, N.280, Y.282, Y.283, D.330, E.334 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.282, E:Y.283 NAG-NAG-BMA-MAN.60: 5 residues within 4Å: Chain F: N.262, N.280, Y.282, Y.283, E.334 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.282, F:Y.283

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.42: 10 residues within 4Å: Chain E: K.200, W.203, D.204, A.205, N.256, N.372, R.374, N.438, S.439 Ligands: NAG-NAG-BMA-MAN-MAN.37 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.204, E:A.205, E:N.438 NAG-NAG-BMA-MAN-MAN-MAN-MAN.63: 9 residues within 4Å: Chain F: K.200, D.204, A.205, N.256, N.372, R.374, N.438, S.439 Ligands: NAG-NAG-BMA-MAN-MAN.58 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.205

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.44: 12 residues within 4Å: Chain E: N.15, S.52, F.53, D.54, F.229, G.270, R.344, K.476 Ligands: NAG-NAG-BMA-MAN.31, NAG-NAG-BMA-MAN.31, NAG-NAG-BMA-MAN-MAN.49, MAN.74 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.344, E:D.54 Hydrophobic interactions: E:F.229

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.73: 3 residues within 4Å: Chain D: D.452, G.453, N.454 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.452 Hydrogen bonds: D:N.454 NAG.75: 3 residues within 4Å: Chain E: D.452, G.453, N.454 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:D.452 NAG.76: 2 residues within 4Å: Chain F: G.453, N.454 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.454

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.74: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.44 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Cryo-EM structures of prefusion SIV envelope trimer. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-16

Peptides

Envelope glycoprotein gp160: ABC
Envelope glycoprotein gp160: DEF
PGT145 Heavy: G
PGT145 Light: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
H

H
L

Envelope glycoprotein gp160

Envelope glycoprotein gp160

PGT145 Heavy

PGT145 Light

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