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- EMDB-3862: FMDV A10 dissociated pentamer -

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Basic information

Entry
Database: EMDB / ID: EMD-3862
TitleFMDV A10 dissociated pentamer
Map data
SampleFMDV A10 dissociated pentamer != Foot-and-mouth disease virus (strain A10-61)

FMDV A10 dissociated pentamer

  • Virus: Foot-and-mouth disease virus (strain A10-61)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
KeywordsA10 / FMDV / Pentamer / CryoEM / virus / VIRAL PROTEIN
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / 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
Biological speciesFoot-and-mouth disease virus (strain A10-61)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsKotecha A / Malik N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099, G1100525/1 United Kingdom
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation.
Authors: Malik N / Kotecha A / Gold S / Asfor A / Ren J / Huiskonen JT / Tuthill TJ / Fry EE / Stuart DI
History
DepositionSep 9, 2017-
Header (metadata) releaseSep 20, 2017-
Map releaseSep 20, 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: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5oyi
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_3862.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.067475475 - 0.117587954
Average (Standard dev.)0.0007149561 (±0.006313616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z270.000270.000270.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0670.1180.001

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Supplemental data

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Sample components

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Entire : FMDV A10 dissociated pentamer

EntireName: FMDV A10 dissociated pentamer
Components
  • Virus: Foot-and-mouth disease virus (strain A10-61)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein

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Supramolecule #1: Foot-and-mouth disease virus (strain A10-61)

SupramoleculeName: Foot-and-mouth disease virus (strain A10-61) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12112
Sci species name: Foot-and-mouth disease virus (strain A10-61)
Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 455 kDa/nm
Virus shellShell ID: 1 / Name: Foot and Disease Virus A1061 / Diameter: 30.0 Å / T number (triangulation number): 3

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase
Source (natural)Organism: Foot-and-mouth disease virus (strain A10-61)
Molecular weightTheoretical: 20.09798 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString:
RHHTDVGFIM DRFVKINSLS PTHVIDLMQT HKHGIVGALL RAATYYFSDL EIVVRHDGNL TWVPNGAPEA ALSNTSNPTA YNKAPFTRL ALPYTAPHRV LATVYDGTNK YSASDSRSGD LGSIAARVAT QLPASFNYGA IQAQAIHELL VRMKRAELYC P RPLLAIKV TSQDRYKQKI IAPA

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase
Source (natural)Organism: Foot-and-mouth disease virus (strain A10-61)
Molecular weightTheoretical: 20.701512 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString:
SVGVTYGYST EEDHVAGPNT SGLETRVVQA ERFFKKFLFD WTTDKPFGYL TKLELPTDHH GVFGHLVDSY AYMRNGWDVE VSAVGNQFN GGCLLVAMVP EWKAFDTREK YQLTLFPHQF ISPRTNMTAH ITVPYLGVNR YDQYKKHKPW TLVVMVLSPL T VSNTAAPQ IKVYANIAPT YVHV

UniProtKB: Genome polyprotein

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase
Source (natural)Organism: Foot-and-mouth disease virus (strain A10-61)
Molecular weightTheoretical: 24.233992 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: GIFPVACADG YGGLVTTDPK TADPVYGKVY NPPKTNYPGR FTNLLDVAEA CPTFLRFDDG KPYVVTRADD TRLLAKFDVS LAAKHMSNT YLSGIAQYYT QYSGTINLHF MFTGSTDSKA RYMVAYIPPG VETPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String:
GIFPVACADG YGGLVTTDPK TADPVYGKVY NPPKTNYPGR FTNLLDVAEA CPTFLRFDDG KPYVVTRADD TRLLAKFDVS LAAKHMSNT YLSGIAQYYT QYSGTINLHF MFTGSTDSKA RYMVAYIPPG VETPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDTAET TNVQGWVCVY QITHGKAEND TLLVSASAGK DFELRLPIDP RTQ

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

Concentration2.5 mg/mL
BufferpH: 8 / Details: 50mM Hepes, 200mM NaCl
GridModel: C-Flats R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 6 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 18 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 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: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 1570 / Average exposure time: 5.0 sec. / Average electron dose: 20.0 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: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1zbe

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 4260
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 1.3)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 200 / Target criteria: Cross-correlation coefficient
Output model

PDB-5oyi:
FMDV A10 dissociated pentamer

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