5EVM

Crystal Structure of Nipah Virus Fusion Glycoprotein in the Prefusion State

  • Classification: VIRAL PROTEIN
  • Organism(s): Nipah virus
  • Expression System: Homo sapiens
  • Mutation(s): 

  • Deposited: 2015-11-20 Released: 2015-12-16 
  • Deposition Author(s): Xu, K., Nikolov, D.B.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Institute of Neurological Disorders and Stroke 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.367 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.

Xu, K.Chan, Y.P.Bradel-Tretheway, B.Akyol-Ataman, Z.Zhu, Y.Dutta, S.Yan, L.Feng, Y.Wang, L.F.Skiniotis, G.Lee, B.Zhou, Z.H.Broder, C.C.Aguilar, H.C.Nikolov, D.B.

(2015) Plos Pathog. 11: e1005322-e1005322

  • DOI: 10.1371/journal.ppat.1005322

  • PubMed Abstract: 
  • Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we repo ...

    Nipah virus (NiV) is a paramyxovirus that infects host cells through the coordinated efforts of two envelope glycoproteins. The G glycoprotein attaches to cell receptors, triggering the fusion (F) glycoprotein to execute membrane fusion. Here we report the first crystal structure of the pre-fusion form of the NiV-F glycoprotein ectodomain. Interestingly this structure also revealed a hexamer-of-trimers encircling a central axis. Electron tomography of Nipah virus-like particles supported the hexameric pre-fusion model, and biochemical analyses supported the hexamer-of-trimers F assembly in solution. Importantly, structure-assisted site-directed mutagenesis of the interfaces between F trimers highlighted the functional relevance of the hexameric assembly. Shown here, in both cell-cell fusion and virus-cell fusion systems, our results suggested that this hexamer-of-trimers assembly was important during fusion pore formation. We propose that this assembly would stabilize the pre-fusion F conformation prior to cell attachment and facilitate the coordinated transition to a post-fusion conformation of all six F trimers upon triggering of a single trimer. Together, our data reveal a novel and functional pre-fusion architecture of a paramyxoviral fusion glycoprotein.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion glycoprotein F0
A, B, C, D, E, F
529Nipah virusMutation(s): 2 
Gene Names: F
Find proteins for Q9IH63 (Nipah virus)
Go to UniProtKB:  Q9IH63
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.367 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.213 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 355.750α = 90.00
b = 355.750β = 90.00
c = 168.859γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-11-20 
  • Released Date: 2015-12-16 
  • Deposition Author(s): Xu, K., Nikolov, D.B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI054715
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI077995
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS38586

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-22
    Type: Refinement description