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- EMDB-3856: Inside-out FMDV A10 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-3856
TitleInside-out FMDV A10 capsid
Map data
SampleInside-out FMDV A10 capsid != Foot-and-mouth disease virus (strain A10-61)

Inside-out FMDV A10 capsid

  • Virus: Foot-and-mouth disease virus (strain A10-61)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
KeywordsVirus / FMDV / A10 / CryoEM / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / regulation of translation / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / 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 / host cell nucleus / virion attachment to host cell / 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 / Peptidase C3A/C3B, picornaviral ...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 / 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 / Papain-like cysteine peptidase superfamily / 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: 5.2 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: 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 4, 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: 0.0488
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0488
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5owx
  • Surface level: 0.0488
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5owx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3856.png

Downloads & links

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Map

FileDownload / File: emd_3856.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0488 / Movie #1: 0.0488
Minimum - Maximum-0.1722611 - 0.2076517
Average (Standard dev.)0.0006698864 (±0.010888514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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/NS000
NC/NR/NS400400400
D min/max/mean-0.1720.2080.001

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Supplemental data

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Sample components

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Entire : Inside-out FMDV A10 capsid

EntireName: Inside-out FMDV A10 capsid
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: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 5.4 MDa
Virus shellShell ID: 1 / Name: FMDV / Diameter: 300.0 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: 1 / Enantiomer: LEVO / EC number: L-peptidase
Source (natural)Organism: Foot-and-mouth disease virus (strain A10-61)
Molecular weightTheoretical: 20.085928 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString:
RHHTDVGFIM DRFVKINSLS PTHVIDLMQT HKHGIVGALL RAATYYFSDL EIVVRHDGNL TWVPNGAPEA ALSNTSNPTA YNKAPFTRL ALPYTAPHRV LATVYDGTNK YSASDSRSGD LGSTAARVAT 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: 1 / 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: 1 / 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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 50mM HEPES, 200mM NaCl, pH 8.0
GridModel: C-FLats / 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: 2-22 / Number grids imaged: 1 / 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: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 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

Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 8077
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)
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-5owx:
Inside-out FMDV A10 capsid

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