SMTL ID : 8tjr.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-2-2-3-3-mer

Ligands

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.1: 11 residues within 4Å: Chain C: K.35, S.179, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.348 NAG-NAG-BMA-MAN-MAN-MAN.4: 10 residues within 4Å: Chain E: K.35, S.179, E.181, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.7: 9 residues within 4Å: Chain I: K.35, S.179, E.181, L.231, N.232, N.346, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.2: 4 residues within 4Å: Chain C: V.144, R.162, N.167 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: T.267, H.299, N.301, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain E: N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, R.412 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain I: N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain I: N.265, C.266, T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: N.308, S.362, W.364 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain C: N.332, S.333, N.355 Ligands: NAG.15, NAG.16 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain C: L.338, T.342, N.355 Ligands: NAG.14 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: S.357, N.361 Ligands: NAG.14 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain C: V.104, N.106, N.118, Y.135 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.271, I.292, Q.408 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.58 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.100, S.101, L.134 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.107, E.110 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain E: N.332, S.333, T.341, N.355 Ligands: NAG.31 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: T.342, N.355 Ligands: NAG.30 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: S.357, N.361 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain E: V.104, N.106, N.118, S.120, Y.135, D.290 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain E: N.265, N.301, R.412, V.414 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: N.271, T.273, Q.408 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain F: N.100, S.102, W.103, I.130 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.105, N.107 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain F: K.122, N.126 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain I: N.204, T.206, S.244 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain I: N.246, T.248, N.249 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain I: N.308, S.362, W.364 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain I: N.332, S.333, T.341, N.355 Ligands: NAG.47, NAG.48 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: N.355 Ligands: NAG.46 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG.46 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain I: N.232, P.261, N.416 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain I: V.104, N.106, N.118, D.290 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain I: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain I: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain I: N.271 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain A: T.59, T.60 Chain I: N.58 Ligand excluded by PLIP NAG.55: 7 residues within 4Å: Chain F: A.1, V.2 Chain H: S.61 Chain J: N.100, W.103, I.130, L.134 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain J: N.105, N.107 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain H: S.57 Chain J: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morano, N.C. et al., CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO HERH-c.01 FAB. To Be Published

Release Date

2024-07-31

Peptides

Antibody HERH-a.01 Heavy Chain: AG
Antibody HERH-a.01 Light Chain: BH
Envelope glycoprotein gp160: CEI
Envelope glycoprotein gp41: DFJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

G
H

B
K

H
L

C
A

E
B

I
C

D
D

F
E

J
F

Antibody HERH-a.01 Heavy Chain

Antibody HERH-a.01 Light Chain

Envelope glycoprotein gp160

Envelope glycoprotein gp41

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