5F1B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1.

Wang, H.Shi, Y.Song, J.Qi, J.Lu, G.Yan, J.Gao, G.F.

(2016) Cell 164: 258-268

  • DOI: 10.1016/j.cell.2015.12.044
  • Primary Citation of Related Structures:  5F18

  • PubMed Abstract: 
  • Filoviruses, including Ebola and Marburg, cause fatal hemorrhagic fever in humans and primates. Understanding how these viruses enter host cells could help to develop effective therapeutics. An endosomal protein, Niemann-Pick C1 (NPC1), has been iden ...

    Filoviruses, including Ebola and Marburg, cause fatal hemorrhagic fever in humans and primates. Understanding how these viruses enter host cells could help to develop effective therapeutics. An endosomal protein, Niemann-Pick C1 (NPC1), has been identified as a necessary entry receptor for this process, and priming of the viral glycoprotein (GP) to a fusion-competent state is a prerequisite for NPC1 binding. Here, we have determined the crystal structure of the primed GP (GPcl) of Ebola virus bound to domain C of NPC1 (NPC1-C) at a resolution of 2.3 Å. NPC1-C utilizes two protruding loops to engage a hydrophobic cavity on head of GPcl. Upon enzymatic cleavage and NPC1-C binding, conformational change in the GPcl further affects the state of the internal fusion loop, triggering membrane fusion. Our data therefore provide structural insights into filovirus entry in the late endosome and the molecular basis for design of therapeutic inhibitors of viral entry.


    Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GP1
A
158Zaire ebolavirus (strain Kikwit-95)Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GP2
B
130Zaire ebolavirus (strain Kikwit-95)Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Niemann-Pick C1 protein
C
256Homo sapiensGene Names: NPC1
Find proteins for O15118 (Homo sapiens)
Go to Gene View: NPC1
Go to UniProtKB:  O15118
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 107.261α = 90.00
b = 107.261β = 90.00
c = 93.777γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHASERphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
China Ministry of Science and Technology National 973 ProjectChina2013CB531502 and 2014CB542503

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references