6UYF
Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 6a bound to broadly neutralizing antibody AR3B
- PDB DOI: https://doi.org/10.2210/pdb6UYF/pdb
- Classification: VIRAL PROEIN/IMMUNE SYSTEM
- Organism(s): Homo sapiens, Recombinant Hepatitis C virus HK6a/JFH-1
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2019-11-13 Released: 2020-04-22 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.06 Å
- R-Value Free: 0.232 
- R-Value Work: 0.189 
- R-Value Observed: 0.191 
wwPDB Validation   3D Report Full Report
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This is version 2.1 of the entry. See complete history. 
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab AR3B heavy chain | A [auth H] | 230 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab AR3B light chain | B [auth L] | 215 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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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] | 177 | Recombinant Hepatitis C virus HK6a/JFH-1 | Mutation(s): 0  | |
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 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 A], E [auth B] | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F [auth C] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG (Subject of Investigation/LOI) Query on NAG | G [auth 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: 2.06 Å
- R-Value Free: 0.232 
- R-Value Work: 0.189 
- R-Value Observed: 0.191 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 175.214 | α = 90 |
b = 54.04 | β = 94.74 |
c = 71.486 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |
SCALEPACK | data scaling |
PHASER | phasing |
Blu-Ice | data collection |
Structure Validation
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Entry History & Funding Information
Deposition Data
- Released Date: 2020-04-22  Deposition Author(s): Tzarum, N., Wilson, I.A., Zhu, J.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI124337 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI129698 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI123861 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI079031 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI123365 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI106005 |
Revision History (Full details and data files)
- Version 1.0: 2020-04-22
Type: Initial release - Version 1.1: 2020-06-17
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary