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- EMDB-3630: CryoEM Structure of Foot and Mouth Disease Virus O PanAsia -

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Basic information

Entry
Database: EMDB / ID: EMD-3630
TitleCryoEM Structure of Foot and Mouth Disease Virus O PanAsia
Map dataCryoEM Map of FMDV O PanAsia
SampleFoot and Mouth Disease Virus O PanAsia != Foot-and-mouth disease virus

Foot and Mouth Disease Virus O PanAsia

  • Virus: Foot-and-mouth disease virus
    • Protein or peptide: O PanAsia VP1
    • Protein or peptide: O PanAsia VP2
    • Protein or peptide: O PanAsia VP3
    • Protein or peptide: O PanAsia VP4
KeywordsFoot and Mouth Disease Virus / FMDV / virus / 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
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 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily ...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 / 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 / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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 / P-loop containing nucleoside triphosphate hydrolase
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKotecha A / Stuart D
Funding support United Kingdom, 3 items
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 alpha v beta 6 integrin and foot-and-mouth disease virus.
Authors: Kotecha A / Wang Q / Dong X / Ilca SL / Ondiviela M / Zihe R / Seago J / Charleston B / Fry EE / Abrescia NGA / Springer TA / Huiskonen JT / Stuart DI
History
DepositionMar 10, 2017-
Header (metadata) releaseMar 22, 2017-
Map releaseJun 21, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ned
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ned
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_3630.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM Map of FMDV O PanAsia
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.16045369 - 0.2585682
Average (Standard dev.)0.00020386043 (±0.015026387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-199-200
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-199-200-200
NC/NR/NS400400400
D min/max/mean-0.1600.2590.000

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Supplemental data

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Sample components

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Entire : Foot and Mouth Disease Virus O PanAsia

EntireName: Foot and Mouth Disease Virus O PanAsia
Components
  • Virus: Foot-and-mouth disease virus
    • Protein or peptide: O PanAsia VP1
    • Protein or peptide: O PanAsia VP2
    • Protein or peptide: O PanAsia VP3
    • Protein or peptide: O PanAsia VP4

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Supramolecule #1: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12110 / Sci species name: Foot-and-mouth disease virus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Name: Foot and Mouth Disease virus / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: O PanAsia VP1

MacromoleculeName: O PanAsia VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.341467 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATA YNGNCKYGES HTTNVRGDLQ VLAQKAARTL P TSFNYGAI ...String:
TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATA YNGNCKYGES HTTNVRGDLQ VLAQKAARTL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPSE ARHKQKIVAP VKQ

UniProtKB: Genome polyprotein

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Macromolecule #2: O PanAsia VP2

MacromoleculeName: O PanAsia VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.389453 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATTE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSINKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATTE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSINKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNTEGAPQIK VYANIAPTNV HVAGEFPSKE

UniProtKB: Genome polyprotein

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Macromolecule #3: O PanAsia VP3

MacromoleculeName: O PanAsia VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.938898 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRILAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String:
GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRILAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDTAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ

UniProtKB: Genome polyprotein

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Macromolecule #4: O PanAsia VP4

MacromoleculeName: O PanAsia VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 8.791128 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSNHTT NTQNNDWFSK LASSAFSGLF GALLA

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Name: HEPES
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 360 / Average exposure time: 5.0 sec. / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13483
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1bbt

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 13483
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 120 / Target criteria: Cross-correlation coefficient
Output model

PDB-5ned:
CryoEM Structure of Foot and Mouth Disease Virus O PanAsia

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