SMTL ID : 7lxm.1

Cryo-EM structure of ConM SOSIP.v7 (ConM) in complex with bNAb PGT122

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN.1: 17 residues within 4Å: Chain A: N.143 Chain C: R.30, D.31, N.32, Y.33, Y.50, H.52, G.55, D.56, T.57, N.58, Y.59, H.100, R.102, W.113 Chain D: W.88, T.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.56, C:D.56, C:G.55, C:N.58 Hydrophobic interactions: C:W.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15: 17 residues within 4Å: Chain E: N.143 Chain G: R.30, D.31, N.32, Y.33, H.52, S.54, G.55, D.56, T.57, N.58, Y.59, H.100, R.102, W.113 Chain H: W.88, T.94 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.56, G:D.56, G:G.55, G:N.58 Hydrophobic interactions: G:W.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.29: 16 residues within 4Å: Chain I: N.143 Chain K: R.30, D.31, N.32, Y.33, Y.50, H.52, G.55, D.56, T.57, N.58, Y.59, H.100, W.113 Chain L: W.88, T.94 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.56, K:G.55, K:N.58 Hydrophobic interactions: K:W.113

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

NAG-NAG.2: 4 residues within 4Å: Chain A: E.92, N.93 Chain B: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.135, C.136, T.137 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.157, K.166 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: F.229, N.230, G.231, T.232, G.233 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: E.88, V.90, N.225, N.237, S.239 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.88, A:V.90 NAG-NAG.8: 6 residues within 4Å: Chain A: N.291, N.327, I.328, S.329, T.394, R.425 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: V.179, P.180, R.188, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: N.272, T.274, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: E.92, N.93 Chain F: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: N.135, C.136, T.137 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: N.157, K.166 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: F.229, N.230, T.232, G.233 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain E: E.88, V.90, N.225, N.237, S.239 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.88, E:V.90 NAG-NAG.22: 4 residues within 4Å: Chain E: N.291, N.327, S.329, T.394 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain E: V.179, R.188, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain E: N.272, T.274, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain I: E.92, N.93 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain I: N.135, C.136, T.137 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain I: N.157, K.166 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain I: F.229, N.230, T.232, G.233 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain I: E.88, V.90, N.225, N.237, S.239 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:E.88, I:V.90 NAG-NAG.36: 4 residues within 4Å: Chain I: N.291, N.327, S.329, T.394 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain I: V.179, R.188, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain I: N.272, T.274, N.275 No protein-ligand interaction detected (PLIP)

3 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.7: 11 residues within 4Å: Chain A: K.70, E.207, V.250, L.257, N.258, N.370, G.372, E.421, T.427, S.428 Ligands: NAG-NAG-BMA.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.372, A:T.427 NAG-NAG-BMA-MAN-MAN-MAN-MAN.21: 11 residues within 4Å: Chain E: K.70, E.207, V.250, L.257, N.258, N.370, G.372, E.421, T.427, S.428 Ligands: NAG-NAG-BMA.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.372, E:T.427 NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 11 residues within 4Å: Chain I: K.70, E.207, V.250, L.257, N.258, N.370, G.372, E.421, T.427, S.428 Ligands: NAG-NAG-BMA.40 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.372, I:T.427

3 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.9: 3 residues within 4Å: Chain A: N.297, I.318, K.423 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 3 residues within 4Å: Chain E: N.297, I.318, K.423 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 3 residues within 4Å: Chain I: N.297, I.318, K.423 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.10: 18 residues within 4Å: Chain A: N.291, T.293, H.325, N.327, T.396, R.425 Chain C: R.103, I.104, G.106, V.107, V.108 Chain D: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 16 residues within 4Å: Chain E: T.293, H.325, N.327, T.396 Chain G: R.103, I.104, G.106, V.107, V.108 Chain H: S.24, N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.38: 15 residues within 4Å: Chain I: T.293, H.325, N.327, T.396 Chain K: R.103, I.104, G.106, V.107, V.108 Chain L: N.44, N.45, N.46, P.60, G.61, S.62 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:V.108

6 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.11: 5 residues within 4Å: Chain A: T.365, T.366, N.379, S.381, R.400 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain A: S.287, T.427, N.429 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain E: T.365, T.366, N.379, S.381, R.400 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 4 residues within 4Å: Chain E: S.287, T.427, N.429 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 5 residues within 4Å: Chain I: T.365, T.366, N.379, S.381, R.400 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 5 residues within 4Å: Chain I: S.287, T.427, S.428, N.429 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.35 No protein-ligand interaction detected (PLIP)

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

NAG.43: 4 residues within 4Å: Chain A: E.264, E.265, N.285, Q.339 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.265 Hydrogen bonds: A:E.264 NAG.44: 1 residues within 4Å: Chain A: N.385 No protein-ligand interaction detected (PLIP) NAG.45: 3 residues within 4Å: Chain B: P.98, W.99, N.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100 NAG.46: 4 residues within 4Å: Chain E: E.264, E.265, N.285, Q.339 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.265 Hydrogen bonds: E:E.264 NAG.47: 1 residues within 4Å: Chain E: N.385 No protein-ligand interaction detected (PLIP) NAG.48: 4 residues within 4Å: Chain F: P.98, W.99, N.100, W.103 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.100 NAG.49: 4 residues within 4Å: Chain I: E.264, E.265, N.285, Q.339 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:E.265 Hydrogen bonds: I:E.264 NAG.50: 1 residues within 4Å: Chain I: N.385 No protein-ligand interaction detected (PLIP) NAG.51: 4 residues within 4Å: Chain J: P.98, W.99, N.100, W.103 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, G.M. et al., Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens. Npj Vaccines (2023)

Release Date

2022-03-09

Peptides

HIV-1 Env glycoprotein gp120: AEI
HIV-1 Env glycoprotein gp41: BFJ
PGT122 Fab heavy chain: CGK
PGT122 Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
E

B
B

F
D

J
F

C
H

G
N

K
P

D
L

H
M

L
O

HIV-1 Env glycoprotein gp120

HIV-1 Env glycoprotein gp41

PGT122 Fab heavy chain

PGT122 Fab light chain

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