SMTL ID : 7ll1.1

Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly neutralizing antibody VRC40.01 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

27 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.1: 5 residues within 4Å: Chain A: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 10 residues within 4Å: Chain A: S.179, E.181, N.232, N.346, C.347, G.348, R.412, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.179, A:S.179, A:G.348, A:R.412 NAG-NAG-BMA.6: 5 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain A: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA.8, NAG-NAG-BMA.8, NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 9 residues within 4Å: Chain A: N.355, T.356, S.357, G.358, L.384, P.385 Ligands: NAG-NAG-BMA.7, NAG-NAG-BMA.7, NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain A: G.358, N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 8 residues within 4Å: Chain A: N.58 Chain B: G.3, I.4, G.16, T.18, D.113, N.114, T.116 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain C: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 8 residues within 4Å: Chain C: N.232, N.346, C.347, G.348, R.412, C.413, V.414, S.415 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.412 NAG-NAG-BMA.16: 6 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain C: N.332, T.341, N.355 Ligands: NAG-NAG-BMA.18, NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 8 residues within 4Å: Chain C: N.355, S.357, G.358, P.385 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 8 residues within 4Å: Chain C: N.58 Chain D: G.3, I.4, G.16, T.18, D.113, N.114, T.116 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain E: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain E: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 8 residues within 4Å: Chain E: E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 6 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain E: N.332, T.341 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 6 residues within 4Å: Chain E: N.355, S.357, G.358 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27, NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 7 residues within 4Å: Chain E: E.57, N.58 Chain F: V.2, G.3, I.4, G.16, D.113 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.113

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.5: 13 residues within 4Å: Chain A: N.246, N.249 Chain G: G.107, F.108, A.111 Chain H: D.30, R.31, S.32, Y.49, S.53, R.54, I.56, Y.92 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:S.53, G:G.107, H:R.54 NAG-NAG-BMA-MAN-MAN-MAN.15: 14 residues within 4Å: Chain C: N.246, T.248, N.249 Chain I: G.107, F.108 Chain J: D.30, R.31, S.32, Y.49, A.50, S.53, R.54, I.56, Y.92 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Y.49, I:G.107, J:R.54 NAG-NAG-BMA-MAN-MAN-MAN.25: 14 residues within 4Å: Chain E: N.246, N.249 Chain K: G.107, F.108, A.111 Chain L: D.30, R.31, S.32, Y.49, A.50, S.53, R.54, I.56, Y.92 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:Y.49, L:S.53, K:G.107, L:R.54

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

NAG.31: 2 residues within 4Å: Chain A: N.103, K.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.117 NAG.32: 2 residues within 4Å: Chain A: N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain A: K.316, N.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.316, A:K.316 NAG.34: 1 residues within 4Å: Chain C: N.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.117 NAG.35: 2 residues within 4Å: Chain C: N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain C: K.316, K.320, N.324 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.316, C:K.316, C:N.324 NAG.37: 2 residues within 4Å: Chain E: N.103, K.117 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.117 NAG.38: 2 residues within 4Å: Chain E: N.308, W.364 No protein-ligand interaction detected (PLIP) NAG.39: 3 residues within 4Å: Chain E: K.316, K.320, N.324 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.316, E:K.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep (2021)

Release Date

2021-03-17

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
VRC40.01 Fab Heavy chain: GIK
VRC40.01 Fab Light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
G

B
B

D
D

F
I

G
H

I
E

K
J

H
L

J
F

L
K

Envelope glycoprotein gp120

Envelope glycoprotein gp41

VRC40.01 Fab Heavy chain

VRC40.01 Fab Light chain

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