5EN2
Molecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses
- PDB DOI: https://doi.org/10.2210/pdb5EN2/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Mus musculus, Mammarenavirus juninense
- Expression System: Mus musculus, Homo sapiens
- Mutation(s): No 
- Deposited: 2015-11-09 Released: 2015-12-30 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.82 Å
- R-Value Free: 0.224 
- R-Value Work: 0.180 
- R-Value Observed: 0.183 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
GD01 heavy chain | 224 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
GD01 light chain | 212 | Mus musculus | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Pre-glycoprotein polyprotein GP complex | 141 | Mammarenavirus juninense | Mutation(s): 0  Gene Names: GPC, GP-C | ||
UniProt | |||||
Find proteins for P26313 (Junin mammarenavirus) Explore P26313  Go to UniProtKB:  P26313 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P26313 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 | D | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | F [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.82 Å
- R-Value Free: 0.224 
- R-Value Work: 0.180 
- R-Value Observed: 0.183 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 52.11 | α = 90 |
b = 74.79 | β = 90 |
c = 177.64 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER-TNT | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-12-30  Deposition Author(s): Mahmutovic, S., Clark, L., Levis, S., Briggiler, A., Enria, D., Harrison, S.C., Abraham, J.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI-109740 |
Revision History (Full details and data files)
- Version 1.0: 2015-12-30
Type: Initial release - Version 1.1: 2017-09-13
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2019-12-11
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary