2VSM

Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Nipah and Hendra Virus Attachment to Their Cell-Surface Receptor Ephrin-B2

Bowden, T.A.Aricescu, A.R.Gilbert, R.J.Grimes, J.M.Jones, E.Y.Stuart, D.I.

(2008) Nat.Struct.Mol.Biol. 15: 567

  • DOI: 10.1038/nsmb.1435
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nipah and Hendra viruses are emergent paramyxoviruses, causing disease characterized by rapid onset and high mortality rates, resulting in their classification as Biosafety Level 4 pathogens. Their attachment glycoproteins are essential for the recog ...

    Nipah and Hendra viruses are emergent paramyxoviruses, causing disease characterized by rapid onset and high mortality rates, resulting in their classification as Biosafety Level 4 pathogens. Their attachment glycoproteins are essential for the recognition of the cell-surface receptors ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3). Here we report crystal structures of both Nipah and Hendra attachment glycoproteins in complex with human EFNB2. In contrast to previously solved paramyxovirus attachment complexes, which are mediated by sialic acid interactions, the Nipah and Hendra complexes are maintained by an extensive protein-protein interface, including a crucial phenylalanine side chain on EFNB2 that fits snugly into a hydrophobic pocket on the viral protein. By analogy with the development of antivirals against sialic acid binding viruses, these results provide a structural template to target antiviral inhibition of protein-protein interactions.


    Organizational Affiliation

    Division of Structural Biology, University of Oxford, Henry Wellcome Building of Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ-NEURAMINIDASE
A
416Nipah virusMutation(s): 0 
Gene Names: G
Find proteins for Q9IH62 (Nipah virus)
Go to UniProtKB:  Q9IH62
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EPHRIN-B2
B
140Homo sapiensMutation(s): 0 
Gene Names: EFNB2 (EPLG5, HTKL, LERK5)
Find proteins for P52799 (Homo sapiens)
Go to Gene View: EFNB2
Go to UniProtKB:  P52799
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.236α = 90.00
b = 95.834β = 90.00
c = 97.909γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Source and taxonomy