SMTL ID : 7t6x.1

Cryo-EM structure of full-length hepatitis C virus E1E2 glycoprotein in complex with AR4A, AT12009, and IGH505 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

2 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: 2 residues within 4Å: Chain A: E.51, N.65 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.312 Chain B: S.133, G.134 No protein-ligand interaction detected (PLIP)

4 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: C.111, G.112, I.113, V.155, N.157 Ligands: NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: D.98, S.118, N.173, S.174, T.175, F.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.98 NAG-NAG-BMA.5: 6 residues within 4Å: Chain A: M.73, A.74, C.237, Y.241, N.262 Ligands: NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.73 NAG-NAG-BMA.9: 6 residues within 4Å: Chain H: N.18, R.105, R.106, H.107, W.108, T.109 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: 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.4: 4 residues within 4Å: Chain A: C.237, I.239, N.240 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP)

2 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.7: 8 residues within 4Å: Chain A: D.270, L.271, E.272 Chain H: S.6, T.7, H.11, C.113, N.114 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A Hydrogen bonds: H:S.6, A:E.272 Hydrophobic interactions: A:E.272 NAG-NAG-BMA-MAN-MAN.8: 5 residues within 4Å: Chain A: Q.84, W.86, V.191 Chain H: N.5, Y.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.191

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

NAG.10: 4 residues within 4Å: Chain A: H.38, N.40, Y.144, W.146 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.144 Hydrogen bonds: A:H.38 NAG.11: 3 residues within 4Å: Chain A: N.47, T.48, S.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.48 NAG.12: 2 residues within 4Å: Chain A: N.93 Ligands: NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain A: N.149, E.150, T.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.151 NAG.14: 1 residues within 4Å: Chain A: N.193 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain H: N.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torrents de la Pena, A. et al., Structure of the hepatitis C virus E1E2 glycoprotein complex. Science (2022)

Release Date

2022-11-02

Peptides

Envelope glycoprotein E2: A
AR4A Fab, heavy chain: B
AR4A, kappa light chain: C
IGH505, heavy chain: D
IGH505, lambda light chain: E
AT12009 crossMab, light kappa chain: F
AT12009 CrossMab, heavy chain: G
Envelope glycoprotein E1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
H

C
L

D
A

E
B

F
D

G
C

H
E

Envelope glycoprotein E2

AR4A Fab, heavy chain

AR4A, kappa light chain

IGH505, heavy chain

IGH505, lambda light chain

AT12009 crossMab, light kappa chain

AT12009 CrossMab, heavy chain

Envelope glycoprotein E1