3CSY
Crystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor
- PDB DOI: https://doi.org/10.2210/pdb3CSY/pdb
- Classification: IMMUNE SYSTEM/VIRAL PROTEIN
- Organism(s): Homo sapiens, Ebola virus - Mayinga, Zaire, 1976
- Expression System: Cricetulus griseus, Homo sapiens
- Mutation(s): Yes 
- Deposited: 2008-04-10 Released: 2008-07-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.302 
- R-Value Work: 0.261 
- R-Value Observed: 0.263 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 |
Fab KZ52 heavy chain | 226 | Homo sapiens | 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 |
Fab KZ52 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein GP1 | 334 | Ebola virus - Mayinga, Zaire, 1976 | Mutation(s): 2  Gene Names: GP | ||
UniProt | |||||
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q05320 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein GP2 | 131 | Ebola virus - Mayinga, Zaire, 1976 | Mutation(s): 0  Gene Names: GP | ||
UniProt | |||||
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q05320 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Q, U, W | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 6 | |||||
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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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | R, V | 5 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 7 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | S | 2 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 8 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | T, X | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G61751GZ GlyCosmos:  G61751GZ GlyGen:  G61751GZ |
Small Molecules
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, C, E, G | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.302 
- R-Value Work: 0.261 
- R-Value Observed: 0.263 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 273.71 | α = 90 |
b = 273.71 | β = 90 |
c = 409.43 | γ = 120 |
Software Name | Purpose |
---|---|
d*TREK | data scaling |
PHASER | phasing |
DM | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
BOS | data collection |
d*TREK | data reduction |
SHARP | phasing |
Entry History 
Deposition Data
- Released Date: 2008-07-08  Deposition Author(s): Lee, J.E., Fusco, M.L., Hessell, A.J., Oswald, W.B., Burton, D.R., Saphire, E.O.
Revision History (Full details and data files)
- Version 1.0: 2008-07-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-03-31
Changes: Source and taxonomy, Structure summary - Version 2.2: 2021-10-20
Changes: Database references, Derived calculations