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 2.0 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: https://doi.org/10.1038/ncomms15408
  • Primary Citation of Related Structures:  
    5NE4, 5NED, 5NEJ, 5NEM, 5NER, 5NET, 5NEU

  • 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 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 ...

    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 VP1A [auth 1]210Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for Q98W00 (Foot-and-mouth disease virus O)
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Go to UniProtKB:  Q98W00
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UniProt GroupQ98W00
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP2B [auth 2]214Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for Q6ZZ87 (Foot-and-mouth disease virus O)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP3C [auth 3]220Foot-and-mouth disease virusMutation(s): 1 
UniProt
Find proteins for Q6ZZ87 (Foot-and-mouth disease virus O)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
O PanAsia VP4D [auth 4]70Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for A6Y878 (Foot-and-mouth disease virus A)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-VE [auth A]594Homo sapiensMutation(s): 0 
Gene Names: ITGAV, MSK8, VNRA, VTNR
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Find proteins for P06756 (Homo sapiens)
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PHAROS:  P06756
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-6F [auth B]470Homo sapiensMutation(s): 0 
Gene Names: ITGB6
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Find proteins for P18564 (Homo sapiens)
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PHAROS:  P18564
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Oligosaccharides

Help

Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranoseG [auth C]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth D]3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth E]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35893LO
GlyCosmos:  G35893LO
GlyGen:  G35893LO
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseJ [auth F]4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G48068RF
GlyCosmos:  G48068RF
GlyGen:  G48068RF
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseK [auth G]4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81874LD
GlyCosmos:  G81874LD
GlyGen:  G81874LD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 7
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900111
Query on PRD_900111		 G [auth C]2alpha-alpha-mannobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.3

Structure Validation

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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  (Full details and data files)

  • 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