SMTL ID : 7txd.1

Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 17 residues within 4Å: Chain A: V.178, S.179, K.222, V.224, L.231, N.232, F.345, N.346, G.348, I.407, G.409, V.410, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.412 NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 17 residues within 4Å: Chain E: V.178, S.179, F.180, E.181, P.182, K.222, L.231, N.232, N.346, G.348, I.407, G.409, V.410, R.412, C.413, V.414 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348

8 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: 6 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA.4, NAG-NAG-BMA.4, NAG-NAG-BMA.4, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 8 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: N.246, I.247, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 6 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 7 residues within 4Å: Chain E: N.332, S.333, T.341, N.355 Ligands: NAG-NAG-BMA.17, NAG-NAG-BMA.17, NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP)

11 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain A: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: G.358, N.361 Ligands: NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.204, T.206, G.207, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: K.320, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: P.261, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.204, T.206 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.206 NAG-NAG.18: 3 residues within 4Å: Chain E: V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain F: N.100, S.102 No protein-ligand interaction detected (PLIP)

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.10: 15 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, L.231, N.232, N.346, C.347, G.348, I.407, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.181, C:G.348

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

NAG.23: 2 residues within 4Å: Chain A: E.57, N.58 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.265, S.303, S.381, R.412 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: K.304, N.308 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: H.299, N.301, S.381, T.383 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.271, N.272 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.430 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.126, Y.127 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: G.323, N.324 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain C: N.308, E.309, S.362, W.364, T.368 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.58 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.265, S.303, S.381, R.412 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: T.267, H.299, N.301 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.361 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.271 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain D: N.100 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.107 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: H.299, N.301, S.381 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: Q.263, N.265, R.412 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.430 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: N.271, R.274 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.204, S.244 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: K.304, N.308, S.362, W.364 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain F: N.107, S.109 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glogl, M. et al., Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-12

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
T-cell surface glycoprotein CD4: GHI
Broadly neutralizing darpin bnd.9: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

Broadly neutralizing darpin bnd.9

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