SMTL ID : 9bew.1

Cryo-EM structure of the HIV-1 BG505 IDL Env trimer in complex with 3BNC117 and 10-1074 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

12 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: 3 residues within 4Å: Chain A: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: R.162, N.167, T.168 Chain C: W.76 Chain M: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.232, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: R.278 Chain G: R.162, N.167, T.168 Chain I: W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain G: N.232, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain M: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain G: R.278 Chain M: R.162, N.167, T.168 Chain O: W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain M: N.232, P.261, N.418 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.20 No protein-ligand interaction detected (PLIP)

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.4: 7 residues within 4Å: Chain A: E.181, L.231, N.232, G.348, V.416, S.417 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.12: 7 residues within 4Å: Chain G: E.181, L.231, N.232, G.348, V.416, S.417 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.20: 7 residues within 4Å: Chain M: E.181, L.231, N.232, G.348, V.416, S.417 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP)

3 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.5: 5 residues within 4Å: Chain A: N.332, T.341, N.355 Ligands: NAG-NAG-BMA-MAN.6, NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 5 residues within 4Å: Chain G: N.332, T.341, N.355 Ligands: NAG-NAG-BMA-MAN.14, NAG-NAG-BMA-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 5 residues within 4Å: Chain M: N.332, T.341, N.355 Ligands: NAG-NAG-BMA-MAN.22, NAG-NAG-BMA-MAN.22 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.6: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5, NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN.13, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 5 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN.21, NAG.59 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.8: 15 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, T.383 Chain E: R.103, I.104, G.106, V.108 Chain F: N.45, N.46, Q.47, P.61, D.62, I.63 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:V.108, A:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.16: 15 residues within 4Å: Chain G: T.267, R.296, H.299, N.301, T.383 Chain K: R.103, I.104, G.106, V.108 Chain L: N.45, N.46, Q.47, P.61, D.62, I.63 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain K Hydrogen bonds: G:R.296, K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 15 residues within 4Å: Chain M: T.267, R.296, H.299, N.301, T.383 Chain Q: R.103, I.104, G.106, V.108 Chain R: N.45, N.46, Q.47, P.61, D.62, I.63 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain M Hydrogen bonds: Q:G.106, Q:V.108, M:R.296

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

NAG.25: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.103, R.113 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: E.245, N.246 Chain D: G.27, Y.28, Y.87 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.271, I.292, V.412 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.308, S.362, W.364 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG-BMA-MAN.6, NAG-NAG-BMA-MAN.6 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: K.199, N.211 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain D: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: E.57, N.58 Chain H: S.17 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.103, R.113 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: N.204, T.206 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain G: E.245, N.246 Chain J: G.27, Y.28, Y.87 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.271, I.292, V.412 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: N.308, S.362, W.364 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG-BMA-MAN.14, NAG-NAG-BMA-MAN.14 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: K.199, N.211 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain H: N.126 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain J: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain M: E.57, N.58 Chain N: S.17 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain M: N.103, R.113 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain M: N.204, T.206 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain M: E.245, N.246 Chain P: G.27, Y.28, Y.87 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain M: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain M: N.271, I.292, V.412 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain M: N.308, S.362, W.364 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain M: S.357, N.361 Ligands: NAG-NAG-BMA-MAN.22, NAG-NAG-BMA-MAN.22 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain M: K.199, N.211 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain N: N.126 Ligand excluded by PLIP NAG.63: 5 residues within 4Å: Chain P: T.20, R.61, W.63, E.66, N.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Rep (2024)

Release Date

2024-07-31

Peptides

Envelope glycoprotein gp120: AGM
Envelope glycoprotein gp41: BHN
3BNC117 heavy chain: CIO
3BNC117 light chain: DJP
10-1074 heavy chain: EKQ
10-1074 light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
A

M
M

B
B

H
E

N
N

C
C

I
F

O
O

D
D

J
I

P
P

E
H

K
J

Q
Q

F
L

L
K

R
R

Envelope glycoprotein gp120

Envelope glycoprotein gp41

3BNC117 heavy chain

3BNC117 light chain

10-1074 heavy chain

10-1074 light chain

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