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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
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation ...L-peptidase / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / 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 / Stuart DI
CitationJournal: PLoS Pathog / Year: 2017
Title: Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation.
Authors: Nayab Malik / Abhay Kotecha / Sarah Gold / Amin Asfor / Jingshan Ren / Juha T Huiskonen / Tobias J Tuthill / Elizabeth E Fry / David I Stuart /
Abstract: Foot-and-mouth disease virus (FMDV) belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious ...Foot-and-mouth disease virus (FMDV) belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5) release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses) have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4), N-termini (VP1) and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers. Here we present the 8-Å resolution structure of isolated dissociated pentamers of FMDV, lacking VP4. We also found these pentamers to re-associate into a rigid, icosahedrally symmetric assembly, which enabled their structure to be solved at higher resolution (5.2 Å). In this assembly, the pentamers unexpectedly associate 'inside out', but still with their exposed hydrophobic edges buried. Stabilizing interactions occur between the HI loop of VP2 and its symmetry related partners at the icosahedral 3-fold axes, and between the BC and EF loops of VP3 with the VP2 βB-strand and the CD loop at the 2-fold axes. A relatively extensive but subtle structural rearrangement towards the periphery of the dissociated pentamer compared to that in the mature virus provides insight into the mechanism of dissociation of FMDV and the marked difference in antigenicity.
History
DepositionSep 9, 2017-
Header (metadata) releaseSep 20, 2017-
Map releaseSep 20, 2017-
UpdateOct 3, 2018-
Current statusOct 3, 2018Processing 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
Supplemental images

emd_3862.png

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 (cattle)
Host systemOrganism: Cricetinae gen. sp. (mammal)
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

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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

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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

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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: 6.0 nm / Pretreatment - Type: GLOW DISCHARGE / 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
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 160000
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
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 - Sampling interval: 5.0 µm / 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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1zbe

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
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
FSC plot (resolution estimation)

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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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