7JTG | pdb_00007jtg

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM11-43

• PDB DOI: https://doi.org/10.2210/pdb7JTG/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Macaca mulatta, Recombinant Hepatitis C virus HK6a/JFH-1
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2020-08-17 Released: 2021-03-10 
• Deposition Author(s): Tzarum, N., 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: 2.60 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

HCV Env immunization elicits a rapid VH1-69-like broadly neutralizing antibody response in rhesus macaques

Tzarum, N., Chen, F., Lin, X., Giang, E., Velazquez-Moctezuma, R., Augestad, E.H., Nagy, K., He, L., Davidson, E., Chavez, D., Prentoe, J., Stanfield, R.L., Lanford, R., Bukh, J., Wilson, I.A., Zhu, J., Law, M.

(2021) Immunity 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.91 kDa 
• Atom Count: 4,517 
• Modeled Residue Count: 582 
• Deposited Residue Count: 636 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM11-43 Fab heavy chain	A	233	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM11-43 Fab light chain	B	214	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein E2	C [auth E]	189	Recombinant Hepatitis C virus HK6a/JFH-1	Mutation(s): 1
UniProt
Find proteins for B9V0E2 (Recombinant Hepatitis C virus HK6a/JFH-1) Explore B9V0E2  Go to UniProtKB:  B9V0E2
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth G]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.956	α = 90
b = 65.343	β = 90
c = 215.871	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Tzarum, N., 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	Al123365
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Al106005

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary