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
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(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.

Macromolecule Content

Total Structure Weight: 360 kDa
Atom Count: 19,278
Modelled Residue Count: 2,409
Deposited Residue Count: 3,201
Unique protein chains: 6

Macromolecules

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Entity ID: 1
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
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Reference Sequence

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Entity ID: 2
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
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Reference Sequence

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Entity ID: 3
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
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Reference Sequence

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Entity ID: 4
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
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Reference Sequence

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Entity ID: 5
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
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Reference Sequence

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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
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Reference Sequence

Oligosaccharides

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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	Interactions Focus chain AA [auth a] Focus chain S [auth K] Focus chain W Interactions & Density Focus chain AA [auth a] Focus chain S [auth K] Focus chain W
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	Interactions Focus chain BA [auth b] Focus chain T [auth R] Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain T [auth R] Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
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	Interactions Focus chain CA [auth c] Focus chain U [auth S] Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain U [auth S] Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
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	Interactions Focus chain DA [auth d] Focus chain V Focus chain Z Interactions & Density Focus chain DA [auth d] Focus chain V Focus chain Z
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 Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth E] SDF format, chain GA [auth F] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth F]	EA [auth A], FA [auth E], GA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth E] Focus chain GA [auth F] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth E] Focus chain GA [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta	2015.19
RECONSTRUCTION	RELION	1.4b1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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5KEL

EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6

Entity ID: 1

UniProt

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Entity ID: 2

UniProt

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Entity ID: 3

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Entity ID: 4

Entity Groups

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)