8F87

Crystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092

• PDB DOI: https://doi.org/10.2210/pdb8F87/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-11-21 Released: 2023-11-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092

Liu, L., Battaile, K.P., Lovell, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 53.5 kDa 
• Atom Count: 2,886 
• Modelled Residue Count: 356 
• Deposited Residue Count: 459 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP1	A	291	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GP2	B	168	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Oligosaccharides

Help

Entity ID: 3
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	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XJ5 (Subject of Investigation/LOI)	H [auth A]	[(4S)-4-amino-3,3-dimethylpiperidin-1-yl][(1S,3R,5R,7S)-3-methyl-5-phenyladamantan-1-yl]methanone C25 H36 N2 O MDGUXHPSSZLCCE-COQNEITCSA-N
NAG	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.199	α = 90
b = 113.199	β = 90
c = 306.021	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	OD030394

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release