6MEJ
Crystal structure of Hepatitis C virus envelope glycoprotein E2 ectodomain in complex with human antibodies HEPC3 and HEPC46
- PDB DOI: https://doi.org/10.2210/pdb6MEJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Hepacivirus hominis
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-09-06 Released: 2018-11-21 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.271 
- R-Value Work: 0.198 
- R-Value Observed: 0.202 
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 |
antibody HEPC46 Heavy Chain | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
antibody HEPC46 Light Chain | 217 | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
E2 glycoprotein | 262 | Hepacivirus hominis | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for C1KH25 (Hepacivirus hominis) Explore C1KH25  Go to UniProtKB:  C1KH25 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | C1KH25 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
antibody HEPC3 Heavy Chain | D [auth H] | 241 | 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: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
antibody HEPC3 Light Chain | E [auth L] | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | F [auth D] | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32708SB GlyCosmos:  G32708SB GlyGen:  G32708SB |
Entity ID: 7 | |||||
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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 | G [auth E] | 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 Query on NAG | H [auth C], I [auth C], J [auth C], K [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.271 
- R-Value Work: 0.198 
- R-Value Observed: 0.202 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 86.44 | α = 90 |
b = 76.64 | β = 106.33 |
c = 118.26 | γ = 90 |
Software Name | Purpose |
---|---|
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHASER | phasing |
Structure Validation
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Currently 6MEJ does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2018-11-21  Deposition Author(s): Flyak, A.I., Bjorkman, P.J.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI127469 |
Revision History (Full details and data files)
- Version 1.0: 2018-11-21
Type: Initial release - Version 1.1: 2018-11-28
Changes: Data collection, Database references - Version 1.2: 2019-11-06
Changes: Data collection, Structure summary - Version 1.3: 2019-12-18
Changes: Author supporting evidence - 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