5F1B

Structural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor Niemann-Pick C1

• PDB DOI: https://doi.org/10.2210/pdb5F1B/pdb

• Classification: VIRAL PROTEIN/TRANSPORT PROTEIN
• Organism(s): Ebola virus - Zaire (1995), Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2015-11-30 Released: 2016-01-20 
• Deposition Author(s): Wang, H., Shi, Y., Song, J., Qi, J., Lu, G., Yan, J., Gao, G.F.
• Funding Organization(s): China Ministry of Science and Technology National 973 Project

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 61.94 kDa 
• Atom Count: 3,828 
• Modelled Residue Count: 460 
• Deposited Residue Count: 544 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP1	A	158	Ebola virus - Zaire (1995)	Mutation(s): 1  Gene Names: GP Membrane Entity: Yes
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666  Go to UniProtKB:  P87666

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GP2	B	130	Ebola virus - Zaire (1995)	Mutation(s): 0  Gene Names: GP Membrane Entity: Yes
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666  Go to UniProtKB:  P87666

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Niemann-Pick C1 protein	C	256	Homo sapiens	Mutation(s): 0  Gene Names: NPC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens) Explore O15118  Go to UniProtKB:  O15118
PHAROS:  O15118 GTEx:  ENSG00000141458

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.261	α = 90
b = 107.261	β = 90
c = 93.777	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Wang, H., Shi, Y., Song, J., Qi, J., Lu, G., Yan, J., Gao, G.F.

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Funding Organization	Location	Grant Number
China Ministry of Science and Technology National 973 Project	China	2013CB531502 and 2014CB542503

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary