5KEL
EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6
- PDB DOI: https://doi.org/10.2210/pdb5KEL/pdb
- EM Map EMD-8240: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Ebola virus - Mayinga, Zaire, 1976, Homo sapiens
- Expression System: Drosophila melanogaster, Nicotiana benthamiana
- Mutation(s): No 
- Deposited: 2016-06-09 Released: 2016-09-07 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 4.30 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 2.0 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 |
Ebola surface glycoprotein, GP1 | A, G [auth E], M [auth F] | 469 | 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Ebola surface glycoprotein, GP2 | B, H [auth G], N [auth I] | 143 | 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
c2G4 variable Fab domain heavy chain | C [auth H], I [auth P], O [auth Q] | 120 | 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: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
c2G4 variable Fab domain light chain | D [auth L], J [auth T], P [auth U] | 107 | 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: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
c13C6 variable Fab domain heavy chain | E [auth C], K [auth J], Q [auth M] | 121 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
c13C6 variable Fab domain light chain | F [auth D], L [auth N], R [auth O] | 107 | 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: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a], S [auth K], W | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 8 | |||||
---|---|---|---|---|---|
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 | BA [auth b], T [auth R], X | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 9 | |||||
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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 | CA [auth c], U [auth S], Y | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 10 | |||||
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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 | DA [auth d], V, Z | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | EA [auth A], FA [auth E], GA [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 4.30 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | Rosetta | 2015.19 |
RECONSTRUCTION | RELION | 1.4b1 |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-09-07  Deposition Author(s): Pallesen, J., Murin, C.D., de Val, N., Cottrell, C.A., Hastie, K.M., Turner, H.L., Fusco, M.L., Flyak, A.I., Zeitlin, L., Crowe Jr., J.E., Andersen, K.G., Saphire, E.O., Ward, A.B.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01 AI067927 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | U19 AI109762 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | U19 AI1097 11 |
Revision History (Full details and data files)
- Version 1.0: 2016-09-07
Type: Initial release - Version 1.1: 2017-09-13
Changes: Author supporting evidence, Data collection - Version 1.2: 2018-07-18
Changes: Data collection, Experimental preparation - Version 1.3: 2019-12-11
Changes: Author supporting evidence, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary