6BZV | pdb_00006bzv

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody 19B3

• PDB DOI: https://doi.org/10.2210/pdb6BZV/pdb

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


• Deposited: 2017-12-26 Released: 2018-06-20 
• Deposition Author(s): Tzarum, N., Aleman, F., Wilson, I.A., Law, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Immunogenetic and structural analysis of a class of HCV broadly neutralizing antibodies and their precursors.

Aleman, F., Tzarum, N., Kong, L., Nagy, K., Zhu, J., Wilson, I.A., Law, M.

(2018) Proc Natl Acad Sci U S A 115: 7569-7574

• PubMed: 29954862 
• DOI: https://doi.org/10.1073/pnas.1802378115
• Primary Citation Related Structures: 
  6BZU, 6BZV, 6BZW, 6BZY


• PubMed Abstract: 
  

  Elicitation of broadly neutralizing antibodies (bnAbs) is a leading strategy in rational vaccine design against antigenically diverse pathogens. Here, we studied a panel of monoclonal antibodies (mAbs) from mice immunized with the hepatitis C virus (HCV) envelope glycoproteins E1E2. Six of the mAbs recognize the conserved E2 antigenic site 412-423 (AS412) and cross-neutralize diverse HCV genotypes. Immunogenetic and structural analysis revealed that the antibodies originated from two different germline (GL) precursors and bind AS412 in a β-hairpin conformation. Intriguingly, the anti-HCV activity of one antibody lineage is associated with maturation of the light chain (LC), whereas the other lineage is dependent on heavy-chain (HC) maturation. Crystal structures of GL precursors of the LC-dependent lineage in complex with AS412 offer critical insights into the maturation process of bnAbs to HCV, providing a scientific foundation for utilizing the mouse model to study AS412-targeting vaccine candidates.

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Organizational Affiliation: 
• Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; [e-mail] [e-mail].
International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037.
Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037.
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037; [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 197.72 kDa 
• Atom Count: 13,683 
• Modeled Residue Count: 1,772 
• Deposited Residue Count: 1,820 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
19B3 GL Heavy Chain	A [auth E], C [auth A], E [auth C], G	223	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19B3 GL Light Chain	B [auth F], D [auth B], F [auth D], H	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 AS412 peptide	I, J, K, L	13	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.128	α = 90
b = 124.767	β = 91.42
c = 102.407	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Tzarum, N., Aleman, F., Wilson, I.A., Law, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI106005
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI123365

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2018-07-25
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-12-18
  Changes: Author supporting evidence
• Version 1.5: 2022-02-02
  Changes: Database references, Structure summary
• Version 1.6: 2024-11-06
  Changes: Data collection, Structure summary