3D12

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3.

Xu, K.Rajashankar, K.R.Chan, Y.P.Himanen, J.P.Broder, C.C.Nikolov, D.B.

(2008) Proc.Natl.Acad.Sci.USA 105: 9953-9958

  • DOI: 10.1073/pnas.0804797105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nipah virus (NiV) and Hendra virus are the type species of the highly pathogenic paramyxovirus genus Henipavirus, which can cause severe respiratory disease and fatal encephalitis infections in humans, with case fatality rates approaching 75%. NiV co ...

    Nipah virus (NiV) and Hendra virus are the type species of the highly pathogenic paramyxovirus genus Henipavirus, which can cause severe respiratory disease and fatal encephalitis infections in humans, with case fatality rates approaching 75%. NiV contains two envelope glycoproteins, the receptor-binding G glycoprotein (NiV-G) that facilitates attachment to host cells and the fusion (F) glycoprotein that mediates membrane merger. The henipavirus G glycoproteins lack both hemagglutinating and neuraminidase activities and, instead, engage the highly conserved ephrin-B2 and ephrin-B3 cell surface proteins as their entry receptors. Here, we report the crystal structures of the NiV-G both in its receptor-unbound state and in complex with ephrin-B3, providing, to our knowledge, the first view of a paramyxovirus attachment complex in which a cellular protein is used as the virus receptor. Complex formation generates an extensive protein-protein interface around a protruding ephrin loop, which is inserted in the central cavity of the NiV-G beta-propeller. Analysis of the structural data reveals the molecular basis for the highly specific interactions of the henipavirus G glycoproteins with only two members (ephrin-B2 and ephrin-B3) of the very large ephrin family and suggests how they mediate in a unique fashion both cell attachment and the initiation of membrane fusion during the virus infection processes. The structures further suggest that the NiV-G/ephrin interactions can be effectively targeted to disrupt viral entry and provide the foundation for structure-based antiviral drug design.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin-neuraminidase
A, D
428Nipah virusMutation(s): 0 
Gene Names: G
Find proteins for Q9IH62 (Nipah virus)
Go to UniProtKB:  Q9IH62
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ephrin-B3
B, E
141Mus musculusMutation(s): 0 
Gene Names: Efnb3
Find proteins for O35393 (Mus musculus)
Go to UniProtKB:  O35393
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NGZ
Query on NGZ

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D
2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-DMHSOCPYSA-N
 Ligand Interaction
MAN
Query on MAN

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A, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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A, D
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GL0
Query on GL0

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A, D
beta-D-gulopyranose
C6 H12 O6
WQZGKKKJIJFFOK-AIECOIEWSA-N
 Ligand Interaction
BMA
Query on BMA

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A, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GLC
Query on GLC

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A, D
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
GXL
Query on GXL

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D
ALPHA-L-GALACTOPYRANOSE
C6 H12 O6
WQZGKKKJIJFFOK-SXUWKVJYSA-N
 Ligand Interaction
LXZ
Query on LXZ

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A
2-(acetylamino)-2-deoxy-alpha-D-idopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-LQOSVEJXSA-N
 Ligand Interaction
LXB
Query on LXB

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D
2-(acetylamino)-2-deoxy-beta-D-gulopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-QQGCVABSSA-N
 Ligand Interaction
NAG
Query on NAG

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A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NGA
Query on NGA

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A
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 189.492α = 90.00
b = 189.492β = 90.00
c = 277.052γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHASESphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-02-12
    Type: Atomic model
  • Version 1.3: 2017-10-25
    Type: Refinement description