7JTG

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.269
R-Value Work: 0.222
R-Value Observed: 0.225

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM11-43 Fab heavy chain	A	233	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM11-43 Fab light chain	B	214	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9V0E2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth E]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth G]	2		N-Glycosylation	Interactions Focus chain D [auth G] Interactions & Density Focus chain D [auth G]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E MOL2 format, chain E mmCIF format, chain E	E	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E Interactions & Density Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.269
R-Value Work: 0.222
R-Value Observed: 0.225
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-10

Deposition Author(s):

Tzarum, N.

Wilson, I.A.

Law, M.

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 (Full details and data files)

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