4G6A | pdb_00004g6a

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody AP33

• PDB DOI: https://doi.org/10.2210/pdb4G6A/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Orthohepacivirus hominis, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-07-18 Released: 2012-09-26 
• Deposition Author(s): Kong, L., Wilson, I.A., Law, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.220 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of Hepatitis C Virus Envelope Glycoprotein E2 Antigenic Site 412 to 423 in Complex with Antibody AP33.

Kong, L., Giang, E., Nieusma, T., Robbins, J.B., Deller, M.C., Stanfield, R.L., Wilson, I.A., Law, M.

(2012) J Virol 86: 13085-13088

• PubMed: 22973046 
• DOI: https://doi.org/10.1128/JVI.01939-12
• Primary Citation Related Structures: 
  4G6A


• PubMed Abstract: 
  

  We have determined the crystal structure of the broadly neutralizing antibody (bnAb) AP33, bound to a peptide corresponding to hepatitis C virus (HCV) E2 envelope glycoprotein antigenic site 412 to 423. Comparison with bnAb HCV1 bound to the same epitope reveals a different angle of approach to the antigen by bnAb AP33 and slight variation in its β-hairpin conformation of the epitope. These structures establish two different modes of binding to E2 that antibodies adopt to neutralize diverse HCV.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.74 kDa 
• Atom Count: 7,073 
• Modeled Residue Count: 901 
• Deposited Residue Count: 910 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 peptide	A [auth B], B [auth A]	13	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for Q9YK84 (Orthohepacivirus hominis) Explore Q9YK84  Go to UniProtKB:  Q9YK84

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP33 Heavy Chain	C, E [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AP33 Light chain	D, F [auth L]	218	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.220 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.875	α = 90
b = 191.804	β = 111.08
c = 59.374	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Kong, L., Wilson, I.A., Law, M.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary