5NER

Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A prime.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rules of engagement between alpha v beta 6 integrin and foot-and-mouth disease virus.

Kotecha, A.Wang, Q.Dong, X.Ilca, S.L.Ondiviela, M.Zihe, R.Seago, J.Charleston, B.Fry, E.E.Abrescia, N.G.A.Springer, T.A.Huiskonen, J.T.Stuart, D.I.

(2017) Nat Commun 8: 15408-15408

  • DOI: 10.1038/ncomms15408
  • Primary Citation of Related Structures:  5NE4, 5NED, 5NEJ, 5NET, 5NEU, 5NEM

  • PubMed Abstract: 
  • Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occ ...

    Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role.


    Organizational Affiliation

    Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O PanAsia VP1
1
210N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
O PanAsia VP2
2
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
O PanAsia VP3
3
220N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
O PanAsia VP4
4
70Foot-and-mouth disease virus - type AN/A
Find proteins for A6Y878 (Foot-and-mouth disease virus - type A)
Go to UniProtKB:  A6Y878
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-V
A
594Homo sapiensGene Names: ITGAV (MSK8, VNRA)
Find proteins for P06756 (Homo sapiens)
Go to Gene View: ITGAV
Go to UniProtKB:  P06756
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-6
B
470Homo sapiensGene Names: ITGB6
Find proteins for P18564 (Homo sapiens)
Go to Gene View: ITGB6
Go to UniProtKB:  P18564
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
1, 2, 3, A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Medical Research Council (United Kingdom)United KingdomG1000099
Medical Research Council (United Kingdom)United KingdomG1100525/1
Wellcome TrustUnited Kingdom090532/Z/09/Z

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Data collection, Experimental preparation, Refinement description
  • Version 1.2: 2017-10-04
    Type: Structure summary