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- EMDB-14183: Cryo-EM structure of coxsackievirus A6 altered particle -

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Basic information

Entry
Database: EMDB / ID: EMD-14183
TitleCryo-EM structure of coxsackievirus A6 altered particle
Map dataSharpened map of CV-A6 altered particle at 2.5 A resolution
Sample
  • Complex: Coxsackievirus A6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesCoxsackievirus A6
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsButtner CR / Spurny R / Fuzik T / Plevka P
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX 19-259882X Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: Commun Biol / Year: 2022
Title: Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion.
Authors: Carina R Büttner / Radovan Spurný / Tibor Füzik / Pavel Plevka /
Abstract: Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous ...Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous structural studies, and it was speculated that the virus is unique among enteroviruses in using altered particles with expanded capsids to infect cells. In contrast, the virions of other enteroviruses are required for infection. Here we used cryo-electron microscopy (cryo-EM) to determine the structures of the CV-A6 virion, altered particle, and empty capsid. We show that the CV-A6 virion has features characteristic of virions of other enteroviruses, including a compact capsid, VP4 attached to the inner capsid surface, and fatty acid-like molecules occupying the hydrophobic pockets in VP1 subunits. Furthermore, we found that in a purified sample of CV-A6, the ratio of infectious units to virions is 1 to 500. Therefore, it is likely that virions of CV-A6 initiate infection, like those of other enteroviruses. Our results provide evidence that future vaccines against CV-A6 should target its virions instead of the antigenically distinct altered particles. Furthermore, the structure of the virion provides the basis for the rational development of capsid-binding inhibitors that block the genome release of CV-A6.
History
DepositionJan 24, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14183.png

Downloads & links

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Map

FileDownload / File: emd_14183.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of CV-A6 altered particle at 2.5 A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 340.16 Å		1.06 Å/pix.
x 320 pix.
= 340.16 Å		1.06 Å/pix.
x 320 pix.
= 340.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6
Minimum - Maximum-9.289571 - 13.710013
Average (Standard dev.)-4.6229403e-09 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 340.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Mask used for calculation of the FSC curve by RELION postprocessing

Fileemd_14183_additional_1.map
AnnotationMask used for calculation of the FSC curve by RELION postprocessing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of CV-A6 altered particle at 2.7 A resolution

Fileemd_14183_additional_2.map
AnnotationUnsharpened map of CV-A6 altered particle at 2.7 A resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ewald sphere corrected half map 1 used in RELION postprocessing

Fileemd_14183_half_map_1.map
AnnotationEwald sphere corrected half map 1 used in RELION postprocessing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ewald sphere corrected half map 2 used in RELION postprocessing

Fileemd_14183_half_map_2.map
AnnotationEwald sphere corrected half map 2 used in RELION postprocessing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Coxsackievirus A6

EntireName: Coxsackievirus A6
Components
  • Complex: Coxsackievirus A6
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Coxsackievirus A6

SupramoleculeName: Coxsackievirus A6 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all / Details: expanded altered CV-A6 particle
Source (natural)Organism: Coxsackievirus A6 / Strain: Gdula
Molecular weightTheoretical: 8 MDa

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1
Details: The first amino-acid of VP1 in the corresponding section of the GenBank polyprotein entry (AAR38844) (Asn) is not the actual first residue as the proteolytic cleavage of the viral ...Details: The first amino-acid of VP1 in the corresponding section of the GenBank polyprotein entry (AAR38844) (Asn) is not the actual first residue as the proteolytic cleavage of the viral polyprotein occurs at an alternative location, leaving the following residue Asp-2 as the first residue (D-1), and the Asn as the additional C-term residue described for VP3 (N-241), as observed in the virion.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 33.530293 KDa
SequenceString: DPISNAIENA VSTLADTTIS RVTAANTAAS SHSLGTGRVP ALQAAETGAS SNASDENLIE TRCVMNRNGV NEASVEHFYS RAGLVGVVE VKDSGTSQDG YTVWPIDVMG FVQQRRKLEL STYMRFDAEF TFVSNLNDST TPGMLLQYMY VPPGAPKPDG R KSYQWQTA ...String:
DPISNAIENA VSTLADTTIS RVTAANTAAS SHSLGTGRVP ALQAAETGAS SNASDENLIE TRCVMNRNGV NEASVEHFYS RAGLVGVVE VKDSGTSQDG YTVWPIDVMG FVQQRRKLEL STYMRFDAEF TFVSNLNDST TPGMLLQYMY VPPGAPKPDG R KSYQWQTA TNPSIFAKLS DPPPQVSVPF MSPASAYQWF YDGYPTFGEH KQATNLQYGQ CPNNMMGHFA IRTVSESTTG KN VHVRVYM RIKHVRAWVP RPFRSQAYMV KNYPTYSQTI SNTAADRASI TTTDYEGGVP ANPQRTF

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 28.006529 KDa
SequenceString: SPSVEACGYS DRVAQLTVGN STITTQEAAN IVLSYGEWPG YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDT GVFGQNAQFH YLYRSGFCMH VQCNASKFHQ GALLVVVIPE FVVAASSPAT KPNGQGLYPD FAHTNPGKEG Q VFRDPYVL ...String:
SPSVEACGYS DRVAQLTVGN STITTQEAAN IVLSYGEWPG YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDT GVFGQNAQFH YLYRSGFCMH VQCNASKFHQ GALLVVVIPE FVVAASSPAT KPNGQGLYPD FAHTNPGKEG Q VFRDPYVL DAGIPLSQAL VFPHQWINLR TNNCATIIMP YVNALPFDSA LNHSNFGLAV IPISPLKYCN GATTEVPITL TI APLNSEF SGLRQAIKQ

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3
Details: VP3 has an additional C-terminal residue (N-241) compared to GenBank entry AAR38844 due to alternative cleavage of the polyprotein as observed in the CV-A6 virion (see compound details for molecule 1 VP1).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 26.489936 KDa
SequenceString: GLPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCRIE TILEVNNTTG TTGVNRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP ...String:
GLPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCRIE TILEVNNTTG TTGVNRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP WISNTHFRAV KTGGVYDYYA TGIVTIWYQT NFVVPPDTPS EANIIALGAA QENFTLKLCK DTDEIRQTAE YQ N

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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: 7.4
Component:
ConcentrationFormulaName
8.0 mg/mLNaClSodium chloridesodium chloride
0.2 mg/mLKClpotassium chloride
1.15 mg/mLNa2HPO4disodium hydrogen phosphate
0.2 mg/mLKH2PO4potassium dihydrogen phosphate

Details: PBS, pH 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.3 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9862 / Average exposure time: 1.0 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 211991
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: INSILICO MODEL / In silico model: stochastic gradient descent (SGD) / Details: RELION 3.1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 33000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 131286
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5xs4

Detailsiterative cycles of building - real space refinement - reciprocal space refinement
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 29 / Target criteria: Correlation coefficient
Output model

PDB-7qvx:
Cryo-EM structure of coxsackievirus A6 altered particle

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