6WOQ

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 1a bound to neutralizing antibody HC1AM and non neutralizing antibody E1

PDB DOI: https://doi.org/10.2210/pdb6WOQ/pdb

Classification: IMMUNE SYSTEM/Viral Protein
Organism(s): Homo sapiens, Hepatitis C virus (isolate H)
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-04-25 Released: 2020-08-19
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: 3.67 Å
R-Value Free: 0.277
R-Value Work: 0.227
R-Value Observed: 0.229

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 236.54 kDa
Atom Count: 14,990
Modelled Residue Count: 1,940
Deposited Residue Count: 2,166
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab E1 heavy chain	A, F [auth C]	227	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab E1 light chain	B, G [auth D]	221	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein E2	C [auth E], H [auth F]	191	Hepatitis C virus (isolate H)	Mutation(s): 0
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958 Go to UniProtKB: P27958
Entity Groups
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UniProt Group	P27958
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab HC1AM heavy chain	D [auth J], I [auth G]	229	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab HC1AM light chain	E [auth K], J [auth H]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth I], L, M, N, O	2		N-Glycosylation	Interactions Focus chain K [auth I] Focus chain L Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain K [auth I] Focus chain L Focus chain M Focus chain N Focus chain O
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 P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth G] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G]	P [auth E], Q [auth F], R [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G] Interactions & Density Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.67 Å
R-Value Free: 0.277
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.744	α = 90
b = 103.721	β = 113.65
c = 196.149	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
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: 2020-08-19

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