SMTL ID : 8top.1

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

9 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: 4 residues within 4Å: Chain A: V.104, N.118, Y.135, L.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.58 Chain B: N.114 Chain M: Y.33, W.106, V.107 Chain N: R.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114 NAG-NAG.5: 5 residues within 4Å: Chain C: N.58 Chain D: N.114 Chain O: Y.33, W.106 Chain P: R.53 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain D Hydrogen bonds: P:R.53, D:N.114 NAG-NAG.7: 6 residues within 4Å: Chain E: N.58 Chain F: N.114 Chain Q: Y.33, W.106, V.107 Chain R: R.53 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.114 NAG-NAG.9: 6 residues within 4Å: Chain G: Y.33, W.106, V.107 Chain J: R.53 Chain S: N.58 Chain T: N.114 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:N.114 NAG-NAG.10: 5 residues within 4Å: Chain U: N.106, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:Y.135 NAG-NAG.12: 6 residues within 4Å: Chain H: Y.33, W.106, V.107 Chain I: R.53 Chain U: N.58 Chain V: N.114 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain V Hydrophobic interactions: H:V.107 Hydrogen bonds: V:N.114, V:N.114 NAG-NAG.13: 3 residues within 4Å: Chain W: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain K: Y.33, W.106, V.107 Chain L: R.53 Chain W: N.58 Chain X: N.114 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:N.114

6 x NAG- NAG- BMA- MAN: 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.2: 11 residues within 4Å: Chain A: P.182, V.224, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN.4: 11 residues within 4Å: Chain C: S.179, K.222, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.348 NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain E: V.224, L.231, N.232, N.346, C.347, C.413, V.414, S.415 Ligands: NAG.52 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.347 NAG-NAG-BMA-MAN.8: 12 residues within 4Å: Chain S: E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.68 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:G.348 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain U: S.179, K.222, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.78 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 8 residues within 4Å: Chain W: S.179, E.181, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.92 2 PLIP interactions: 2 interactions with chain W Hydrophobic interactions: W:V.414 Hydrogen bonds: W:G.348, W:S.179, W:S.179

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

NAG.16: 2 residues within 4Å: Chain A: N.103, G.114 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.122, K.133 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: R.162, N.167, T.168 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.204, T.206, P.208, H.321 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.246, T.248 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: T.267, H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.22: 8 residues within 4Å: Chain A: N.332, S.333, S.334, G.335, T.341, S.357 Ligands: NAG.23, NAG.26 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: T.341, T.342, N.355, S.357 Ligands: NAG.22 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: Q.263, N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG.22 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.271, T.273, I.292 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: N.118, Y.135, L.137, G.289, D.290 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: Q.100, N.122, K.133 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: R.162, I.164, N.167, T.168 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: T.267, H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: N.332, S.333, S.334 Ligands: NAG.37, NAG.38 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: N.332, T.341, N.355, S.357 Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: R.329, N.361 Ligands: NAG.36 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.41: 8 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, S.381, R.412, V.414 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain D: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.107 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: C.101, N.103 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: D.129 Chain E: T.98, Q.100, N.122, K.133 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: V.144, R.162, N.167 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: N.204, S.244 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.246, T.248 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: N.271, I.292 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain E: T.267, H.299, N.301, T.383 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: T.341, N.355, S.357 Ligands: NAG.55 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.6 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: Q.263, N.265, S.303, R.412 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: N.118, Y.135, L.137 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: N.332, S.333, S.334 Ligands: NAG.51 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.107, S.109 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain S: N.103, G.114 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain S: N.118, Y.135, L.137, D.290 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain S: T.98, Q.100, N.122, K.133 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain S: R.162, N.167 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain S: N.204, T.206, S.244 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain S: N.246, T.248 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain S: N.271, I.292, V.410 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain S: T.267, H.299, N.301, T.383 Ligand excluded by PLIP NAG.65: 7 residues within 4Å: Chain S: N.332, S.333, S.334, T.341, S.357 Ligands: NAG.66, NAG.67 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain S: N.355, S.357 Ligands: NAG.65 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain S: N.361 Ligands: NAG.65 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain S: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.8 Ligand excluded by PLIP NAG.69: 4 residues within 4Å: Chain S: N.308, S.362, T.363, W.364 Ligand excluded by PLIP NAG.70: 3 residues within 4Å: Chain S: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.71: 4 residues within 4Å: Chain U: C.101, T.102, N.103, K.117 Ligand excluded by PLIP NAG.72: 5 residues within 4Å: Chain S: D.129 Chain U: T.98, Q.100, N.122, K.133 Ligand excluded by PLIP NAG.73: 4 residues within 4Å: Chain U: N.204, T.206, P.208, S.244 Ligand excluded by PLIP NAG.74: 2 residues within 4Å: Chain U: N.246, N.249 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain U: N.271, I.292 Ligand excluded by PLIP NAG.76: 4 residues within 4Å: Chain U: T.267, H.299, N.301, T.383 Ligand excluded by PLIP NAG.77: 3 residues within 4Å: Chain U: N.355, S.357 Ligands: NAG.82 Ligand excluded by PLIP NAG.78: 4 residues within 4Å: Chain U: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain U: K.304, N.308, W.364 Ligand excluded by PLIP NAG.80: 4 residues within 4Å: Chain U: Q.263, N.265, S.303, R.412 Ligand excluded by PLIP NAG.81: 3 residues within 4Å: Chain U: R.162, N.167, T.168 Ligand excluded by PLIP NAG.82: 5 residues within 4Å: Chain U: N.332, S.333, T.341, S.357 Ligands: NAG.77 Ligand excluded by PLIP NAG.83: 1 residues within 4Å: Chain V: N.126 Ligand excluded by PLIP NAG.84: 3 residues within 4Å: Chain V: N.107, S.109, E.110 Ligand excluded by PLIP NAG.85: 1 residues within 4Å: Chain W: N.103 Ligand excluded by PLIP NAG.86: 3 residues within 4Å: Chain W: Q.100, N.122, K.133 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain W: N.246, T.248 Ligand excluded by PLIP NAG.88: 3 residues within 4Å: Chain W: N.271, I.292, Q.408 Ligand excluded by PLIP NAG.89: 5 residues within 4Å: Chain W: N.265, T.267, H.299, N.301, T.383 Ligand excluded by PLIP NAG.90: 4 residues within 4Å: Chain W: T.341, N.355, S.357 Ligands: NAG.91 Ligand excluded by PLIP NAG.91: 3 residues within 4Å: Chain W: S.357, N.361 Ligands: NAG.90 Ligand excluded by PLIP NAG.92: 5 residues within 4Å: Chain W: N.232, P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN.14 Ligand excluded by PLIP NAG.93: 2 residues within 4Å: Chain W: K.304, N.308 Ligand excluded by PLIP NAG.94: 4 residues within 4Å: Chain W: Q.263, N.265, S.303, V.414 Ligand excluded by PLIP NAG.95: 4 residues within 4Å: Chain W: N.106, N.118, Y.135, L.137 Ligand excluded by PLIP NAG.96: 2 residues within 4Å: Chain W: R.162, N.167 Ligand excluded by PLIP NAG.97: 3 residues within 4Å: Chain X: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H., Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide. To Be Published

Release Date

2024-08-07

Peptides

HIV-1 BG505 DS-SOSIP gp120: ACESUW
HIV-1 BG505 DS-SOSIP glycoprotein gp41: BDFTVX
Heavy chain of antibody GPZ6-b.01: GHKMOQ
Light chain of antibody GPZ6-b.01: IJLNPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

E
S

S
A

U
C

W
E

B
P

D
R

F
T

T
B

V
D

X
F

G
H

H
J

K
M

M
U

O
W

Q
Y

I
K

J
L

L
N

N
V

P
X

R
Z

HIV-1 BG505 DS-SOSIP gp120

HIV-1 BG505 DS-SOSIP glycoprotein gp41

Heavy chain of antibody GPZ6-b.01

Light chain of antibody GPZ6-b.01

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