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
Deposition Author(s): Lee, J.E., Fusco, M.L., Hessell, A.J., Oswald, W.B., Burton, D.R., Saphire, E.O.

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.

Macromolecule Content

Total Structure Weight: 406.07 kDa
Atom Count: 23,539
Modelled Residue Count: 3,074
Deposited Residue Count: 3,632
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab KZ52 heavy chain	A, C, E, G	226	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab KZ52 light chain	B, D, F, H	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein GP1	I, K, M, O	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 Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein GP2	J, L, N, P	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 Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain Q Focus chain U Focus chain W Interactions & Density Focus chain Q Focus chain U Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	R, V	5		N/A	Interactions Focus chain R Focus chain V Interactions & Density Focus chain R Focus chain V
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	S	2		N/A	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
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	Interactions Focus chain T Focus chain X Interactions & Density Focus chain T Focus chain X
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 Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-07-08

Deposition Author(s):

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