5NET

Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 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. 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O1 Manisa VP1A [auth 1]208Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for Q6PMW3 (Foot-and-mouth disease virus O)
Explore Q6PMW3 
Go to UniProtKB:  Q6PMW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PMW3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
O1 Manisa VP2B [auth 2]218Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for D1H101 (Foot-and-mouth disease virus)
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Go to UniProtKB:  D1H101
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1H101
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
O1 Manisa VP3C [auth 3]220Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for Q6PMW3 (Foot-and-mouth disease virus O)
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Go to UniProtKB:  Q6PMW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PMW3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
O1 Manisa VP4D [auth 4]85Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for D1H101 (Foot-and-mouth disease virus)
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Go to UniProtKB:  D1H101
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1H101
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-VE [auth A]594Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRA
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens)
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Go to UniProtKB:  P06756
PHAROS:  P06756
GTEx:  ENSG00000138448 
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UniProt GroupP06756
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-6F [auth B]470Homo sapiensMutation(s): 0 
Gene Names: ITGB6
UniProt & NIH Common Fund Data Resources
Find proteins for P18564 (Homo sapiens)
Explore P18564 
Go to UniProtKB:  P18564
PHAROS:  P18564
GTEx:  ENSG00000115221 
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UniProt GroupP18564
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C],
H [auth D]
3N/A
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranoseI [auth E]2N/A
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Entity ID: 9
MoleculeChains 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-glucopyranoseJ [auth F]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF
GlyCosmos:  G48068RF
GlyGen:  G48068RF
Entity ID: 10
MoleculeChains 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-glucopyranoseK [auth G]4N/A
Glycosylation Resources
GlyTouCan:  G81874LD
GlyCosmos:  G81874LD
GlyGen:  G81874LD
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth A],
T [auth B],
U [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
L [auth 3],
M [auth 3],
N [auth A]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.3

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  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Experimental preparation, Refinement description
  • Version 1.2: 2017-10-04
    Changes: Structure summary
  • Version 1.3: 2018-03-28
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary