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



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:  
    5NED, 5NEJ, 5NE4, 5NEU, 5NET, 5NEM, 5NER

  • 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

    Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP11210Foot-and-mouth disease virusMutation(s): 0 
Find proteins for Q98W00 (Foot-and-mouth disease virus - type O)
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Go to UniProtKB:  Q98W00
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP22214Foot-and-mouth disease virusMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
Find proteins for Q6ZZ87 (Foot-and-mouth disease virus - type O)
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Go to UniProtKB:  Q6ZZ87
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP33220Foot-and-mouth disease virusMutation(s): 1 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
Find proteins for Q6ZZ87 (Foot-and-mouth disease virus - type O)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP4470Foot-and-mouth disease virusMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
Find proteins for A6Y878 (Foot-and-mouth disease virus - type A)
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Go to UniProtKB:  A6Y878
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-VA594Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
Find proteins for P06756 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P06756
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-6B470Homo sapiensMutation(s): 0 
Gene Names: ITGB6
Find proteins for P18564 (Homo sapiens)
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Go to UniProtKB:  P18564
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PHAROS  P18564
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
C
2 N/A Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3 N/A Oligosaccharides Interaction
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2 N/A Oligosaccharides Interaction
Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
4 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 7
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900111
Query on PRD_900111
C2alpha-alpha-mannobioseOligosaccharide /  Metabolism

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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



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
    Changes: Data collection, Experimental preparation, Refinement description
  • Version 1.2: 2017-10-04
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary