SMTL ID : 7tfo.1

Cryo-EM structure of HIV-1 Env trimer BG505 SOSIP.664 in complex with CD4bs antibody Ab1573

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

1 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: 5 residues within 4Å: Chain A: N.355, S.357, R.387 Chain G: Y.31 Ligands: NAG-NAG-BMA.2 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.2: 4 residues within 4Å: Chain A: N.332, S.333, S.357 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: N.246, T.248, N.249 Chain I: D.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.248

1 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.4: 8 residues within 4Å: Chain A: S.179, E.181, P.182, L.231, N.232, G.348, V.414, S.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.414

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

NAG.6: 5 residues within 4Å: Chain A: I.146, R.162, N.167, T.168 Chain D: Q.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.162, A:N.167 NAG.7: 3 residues within 4Å: Chain B: N.246, T.248, N.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.246, B:T.248, B:N.249 NAG.8: 4 residues within 4Å: Chain B: N.332, S.357 Chain F: E.30, G.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.332, B:S.357 NAG.9: 2 residues within 4Å: Chain C: R.162, N.167 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.162, C:N.167 NAG.10: 7 residues within 4Å: Chain C: N.332, S.333, S.334, G.335, T.341, S.357 Chain I: E.30 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer. Nat Commun (2022)

Release Date

2022-01-26

Peptides

Envelope glycoprotein BG505 SOSIP.664 - gp120: ABC
CD4 binding site antibody Ab1573 - Fab heavy chain: DEH
CD4 binding site antibody Ab1573 - Fab light chain: FGI
Envelope glycoprotein BG505 SOSIP.664 - gp41: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

H
P

F
J

G
L

I
Q

J
X

K
Y

L
Z

Envelope glycoprotein BG505 SOSIP.664 - gp120

CD4 binding site antibody Ab1573 - Fab heavy chain

CD4 binding site antibody Ab1573 - Fab light chain

Envelope glycoprotein BG505 SOSIP.664 - gp41

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