SMTL ID : 8tl5.1

CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO HERH-c.01 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

NAG-NAG.1: 4 residues within 4Å: Chain A: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.355, S.357 Ligands: 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: 5 residues within 4Å: Chain A: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.332, T.341 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.265, S.303 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: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.246, 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: 4 residues within 4Å: Chain C: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: N.332, T.341 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.30, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain E: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain E: N.332, T.341 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: N.58 Chain B: N.114 Chain G: W.108, K.109 Chain H: N.30, L.31, W.32, G.50 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:N.114, G:K.109, G:K.109, B:N.114 NAG-NAG-BMA.14: 8 residues within 4Å: Chain C: N.58 Chain D: N.114, T.116 Chain I: W.108, K.109 Chain J: N.30, L.31, W.32 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:N.114, I:K.109, D:N.114 NAG-NAG-BMA.24: 8 residues within 4Å: Chain E: N.58 Chain F: N.114 Chain K: W.108, K.109 Chain L: N.30, L.31, W.32, G.50 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:K.109, F:N.114

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: 11 residues within 4Å: Chain A: S.179, E.181, P.182, N.232, R.274, N.346, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:G.348, A:R.274, A:Q.408 NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, N.232, R.274, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.414 Hydrogen bonds: C:G.348, C:Q.408 NAG-NAG-BMA-MAN-MAN.27: 9 residues within 4Å: Chain E: S.179, E.181, P.182, N.232, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG.22 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.414 Hydrogen bonds: E:G.348, E:V.414, E:Q.408

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.31: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.271, I.292 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: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.204, T.206 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: S.357, G.358, N.361 Ligands: 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: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: N.204, T.206 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: S.357, N.361 Ligands: NAG-NAG.26, NAG-NAG.26 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.271, I.292 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: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H., Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques. To Be Published

Release Date

2024-08-28

Peptides

BG505 DS-SOSIP Surface protein gp120: ACE
BG505 DS-SOSIP Transmembrane protein gp41: BDF
HERH-c.01 FAB HEAVY CHAIN: GIK
HERH-c.01 FAB 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

BG505 DS-SOSIP Surface protein gp120

BG505 DS-SOSIP Transmembrane protein gp41

HERH-c.01 FAB HEAVY CHAIN

HERH-c.01 FAB LIGHT CHAIN

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