SMTL ID : 7lxn.1

Cryo-EM structure of EDC-crosslinked ConM SOSIP.v7 (ConM-EDC) 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: 15 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, K.64, H.100, W.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.56, C:T.57 Hydrophobic interactions: C:W.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15: 16 residues within 4Å: Chain E: N.143 Chain G: R.30, D.31, N.32, Y.33, Y.50, H.52, G.55, D.56, T.57, N.58, Y.59, K.64, H.100, W.113 Chain H: T.94 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.56, G:T.57 Hydrophobic interactions: G:W.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.29: 14 residues within 4Å: Chain I: N.143 Chain K: R.30, D.31, Y.33, Y.50, H.52, G.55, D.56, T.57, N.58, Y.59, K.64, H.100, W.113 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.56, K:T.57, K:K.64, 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: 5 residues within 4Å: Chain A: E.92, N.93 Chain B: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.135, T.137, S.155 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, T.232, G.233, P.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.232 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: 3 residues within 4Å: Chain A: N.291, N.327, S.329 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: R.188, N.193, T.194 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: 5 residues within 4Å: Chain E: E.92, N.93 Chain F: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.135, T.137, S.155, K.168 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: 5 residues within 4Å: Chain E: F.229, N.230, T.232, G.233, P.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.232 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: 3 residues within 4Å: Chain E: N.291, N.327, S.329 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain E: R.188, N.193, T.194 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: 5 residues within 4Å: Chain I: E.92, N.93 Chain J: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain I: N.135, T.137, S.155 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: 5 residues within 4Å: Chain I: F.229, N.230, T.232, G.233, P.234 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.232 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: 3 residues within 4Å: Chain I: N.291, N.327, S.329 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain I: R.188, N.193, T.194 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: 12 residues within 4Å: Chain A: K.70, S.205, E.207, P.208, V.250, L.257, N.258, N.370, G.372, T.427, S.428 Ligands: NAG-NAG-BMA.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.372, A:T.427, A:T.427 NAG-NAG-BMA-MAN-MAN-MAN-MAN.21: 11 residues within 4Å: Chain E: K.70, S.205, P.208, V.250, L.257, N.258, N.370, G.372, T.427, S.428 Ligands: NAG-NAG-BMA.26 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.372, E:T.427, E:T.427 NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 11 residues within 4Å: Chain I: K.70, S.205, E.207, V.250, L.257, N.258, N.370, G.372, T.427, S.428 Ligands: NAG-NAG-BMA.40 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:G.372, I:T.427, 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: 14 residues within 4Å: Chain A: N.291, T.293, H.325, N.327, T.396 Chain C: R.103, I.104, V.108 Chain D: S.24, N.44, N.45, N.46, P.60, G.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 13 residues within 4Å: Chain E: N.291, T.293, H.325, N.327 Chain G: R.103, I.104, G.106, V.108 Chain H: N.44, N.45, N.46, P.60, G.61 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.38: 12 residues within 4Å: Chain I: N.291, T.293, H.325, N.327 Chain K: I.104, G.106, V.108 Chain L: N.44, N.45, N.46, 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: 4 residues within 4Å: Chain A: T.365, T.366, N.379, S.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain A: S.287, T.427, S.428, N.429 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 4 residues within 4Å: Chain E: T.365, T.366, N.379, S.381 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 5 residues within 4Å: Chain E: S.287, T.427, S.428, N.429 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 4 residues within 4Å: Chain I: T.365, T.366, N.379, S.381 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, I.266, N.285, Q.339 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.266 Hydrogen bonds: A:E.264, A:N.285 NAG.44: 1 residues within 4Å: Chain A: N.385 No protein-ligand interaction detected (PLIP) NAG.45: 5 residues within 4Å: Chain B: P.98, W.99, N.100, S.102, W.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.100, B:S.102 NAG.46: 4 residues within 4Å: Chain E: E.264, I.266, N.285, Q.339 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.266 Hydrogen bonds: E:E.264, E:N.285 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 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:P.98, F:W.103 Hydrogen bonds: F:N.100 NAG.49: 4 residues within 4Å: Chain I: E.264, I.266, N.285, Q.339 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:I.266 Hydrogen bonds: I:E.264, I:N.285 NAG.50: 1 residues within 4Å: Chain I: N.385 No protein-ligand interaction detected (PLIP) NAG.51: 5 residues within 4Å: Chain J: P.98, W.99, N.100, S.102, W.103 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:P.98 Hydrogen bonds: J:S.102

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
I

K
J

D
L

H
M

L
N

HIV-1 Env glycoprotein gp120

HIV-1 Env glycoprotein gp41

PGT122 Fab heavy chain

PGT122 Fab light chain

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