SMTL ID : 8fsj.1

Cryo-EM structure of engineered hepatitis C virus E1E2 ectodomain in complex with antibodies AR4A, HEPC74, and IGH520

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 4 residues within 4Å: Chain A: N.47, S.49 Chain C: S.53, T.56 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: G.112, T.113, N.157 No protein-ligand interaction detected (PLIP)

6 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.3: 8 residues within 4Å: Chain A: N.65, S.67 Chain B: Q.1, S.25, G.26, G.27, Y.29, I.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.25, B:S.25, B:Q.1 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: A.66, C.237, N.240 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain A: M.73, C.76, C.237, F.241, N.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.73, A:A.74 NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: Q.118, N.173, S.174, T.175, F.177, K.179 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain A: L.271, Q.272 Chain D: R.4, S.7, H.11, N.114 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.4, D:S.7 Hydrophobic interactions: A:Q.272 NAG-NAG-BMA.8: 5 residues within 4Å: Chain A: Q.84, W.86, V.191 Chain D: 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.9: 2 residues within 4Å: Chain A: N.193, N.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194 NAG.10: 4 residues within 4Å: Chain A: Q.311, N.312 Chain F: S.135, G.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.311 NAG.11: 2 residues within 4Å: Chain A: N.149, T.151 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.40 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain D: N.18, H.107, E.108, T.109 No protein-ligand interaction detected (PLIP) NAG.14: 5 residues within 4Å: Chain D: D.27, N.59, S.61, V.62, P.63 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.59, D:V.62 Hydrogen bonds: D:V.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metcalf, M.C. et al., Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies. Nat Commun (2023)

Release Date

2023-07-19

Peptides

HCV E2 ectodomain, SYNZIP2 scaffold fusion: A
HEPC74 heavy chain: B
HEPC74 light chain: C
HCV E1 ectodomain, SYNZIP1 scaffold fusion: D
AR4A light chain: E
AR4A heavy chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

D
A

E
B

F
C

HCV E2 ectodomain, SYNZIP2 scaffold fusion

HEPC74 heavy chain

HEPC74 light chain

HCV E1 ectodomain, SYNZIP1 scaffold fusion

AR4A light chain

AR4A heavy chain

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