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- PDB-5ne4: Crystal Structure of Foot and Mouth Disease Virus O PanAsia -

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Basic information

Entry
Database: PDB / ID: 5ne4
TitleCrystal Structure of Foot and Mouth Disease Virus O PanAsia
Components
  • O PanAsia VP1
  • O PanAsia VP2
  • O PanAsia VP4
  • Polyprotein
KeywordsVIRUS / Foot and Mouth Disease Virus / FMDV / OpanAsia
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
Foot-and-mouth disease virus - type O
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKotecha, A. / StuarT, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Medical Research Council (United Kingdom)G1100525/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus.
Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T ...Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T Huiskonen / David I Stuart /
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, ...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.
History
DepositionMar 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: O PanAsia VP1
2: O PanAsia VP2
3: Polyprotein
4: O PanAsia VP4


Theoretical massNumber of molelcules
Total (without water)80,4624
Polymers80,4624
Non-polymers00
Water1,982110
1
1: O PanAsia VP1
2: O PanAsia VP2
3: Polyprotein
4: O PanAsia VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,827,716240
Polymers4,827,716240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: O PanAsia VP1
2: O PanAsia VP2
3: Polyprotein
4: O PanAsia VP4
x 5


  • icosahedral pentamer
  • 402 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)402,31020
Polymers402,31020
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: O PanAsia VP1
2: O PanAsia VP2
3: Polyprotein
4: O PanAsia VP4
x 6


  • icosahedral 23 hexamer
  • 483 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)482,77224
Polymers482,77224
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)345.010, 345.010, 345.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein O PanAsia VP1


Mass: 23341.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Strain: O / Variant: PanAsia / Cell line (production host): BHK-21 / Production host: Cricetinae (hamsters) / References: UniProt: A0A1B0SZV3, UniProt: Q98W00*PLUS
#2: Protein O PanAsia VP2


Mass: 24389.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Strain: O / Variant: PanAsia / Cell line (production host): BHK-21 / Production host: Cricetinae (hamsters) / References: UniProt: A0A1B0QWS1, UniProt: Q6ZZ87*PLUS
#3: Protein Polyprotein


Mass: 23938.898 Da / Num. of mol.: 1 / Mutation: H56R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Variant: PanAsia / Cell line (production host): BHK-21 / Production host: Cricetinae (hamsters) / References: UniProt: J3T9N5, UniProt: Q7TD07*PLUS
#4: Protein O PanAsia VP4


Mass: 8792.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Variant: PanAsia / Cell line (production host): BHK-21 / Production host: Cricetinae (hamsters) / References: UniProt: E6Y5R5, UniProt: Q7TD07*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5 M ammonium sulfate, 100 mM bis-Tris propane, pH 7.0.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 229892 / % possible obs: 76.9 % / Observed criterion σ(I): 0.86 / Redundancy: 2.1 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 3.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.88 / % possible all: 45.9

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Processing

Software
NameVersionClassification
CNSv1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBT

1bbt


Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.22 11647 3.9 %Random
Rwork0.21 ---
obs-229892 76.9 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1 Å / Bsol: 24.4454 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 20.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 0 110 5199

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