SMTL ID : 8euv.1

Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 8 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, N.379, R.412, V.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.379 NAG-NAG.2: 5 residues within 4Å: Chain A: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10, NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.265, T.267, H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.20, NAG-NAG.20, NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.265, T.267, H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 7 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 8 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, N.379, R.412, V.414 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.379 NAG-NAG.22: 5 residues within 4Å: Chain E: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.30, NAG-NAG.30, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain E: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain E: N.265, T.267, H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 7 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP)

3 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.4: 8 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain G: Y.102 Chain H: N.31, Y.49, Y.50 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.31 NAG-NAG-BMA.14: 7 residues within 4Å: Chain C: N.58 Chain D: G.16, S.17 Chain I: Y.102 Chain J: Y.49, Y.50, T.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 7 residues within 4Å: Chain E: N.58 Chain F: G.16, S.17 Chain K: Y.102 Chain L: N.31, Y.49, Y.50 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.31

3 x NAG- NAG- BMA- MAN- MAN: 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.7: 12 residues within 4Å: Chain A: S.179, E.181, P.182, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.414, A:Q.408, A:Q.408 NAG-NAG-BMA-MAN-MAN.17: 13 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.414, C:Q.408 NAG-NAG-BMA-MAN-MAN.27: 13 residues within 4Å: Chain E: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.414, E:Q.408, E:Q.408

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

NAG.31: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: R.162, N.167 Chain C: R.278 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.103, R.113 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.204 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: S.357, G.358, N.361 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.103, R.113, G.114 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain E: N.204 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain E: S.357, G.358, N.361 Ligands: NAG-NAG.26, NAG-NAG.26 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.103, R.113, G.114 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banach, B.B. et al., Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site. Nat Commun (2023)

Release Date

2023-09-27

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
VRC34.01-COMBO1 FAB variable heavy chain: GIK
VRC34.01-COMBO1 FAB variable light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

I
I

K
K

H
H

J
J

L
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

VRC34.01-COMBO1 FAB variable heavy chain

VRC34.01-COMBO1 FAB variable light chain

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