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- EMDB-6752: Structure of Coxsackievirus A6 (CVA6) virus procapsid particle -

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Basic information

Entry
Database: EMDB / ID: 6752
TitleStructure of Coxsackievirus A6 (CVA6) virus procapsid particle
Map data
SampleCoxsackievirus A6:
virus / (Genome polyprotein) x 3
Function / homologyPeptidase C3A/C3B, picornaviral / picornavirus capsid protein / Protein of unknown function DUF3724, picornavirus / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein ...Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Protein of unknown function DUF3724, picornavirus / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / Picornavirus core protein 2A / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Protein of unknown function (DUF3724) / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / RNA helicase / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphatase / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / suppression by virus of host gene expression / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / structural molecule activity / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceCoxsackievirus A6
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsZheng QB / He MZ
CitationJournal: Nat Commun / Year: 2017
Title: Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.
Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng Hou / Wei Wang / Xiangzhong Ye / Jun Zhang / Timothy S Baker / Tong Cheng / Z Hong Zhou / Xiaodong Yan / Ningshao Xia
Validation ReportPDB-ID: 5xs5

SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0915
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0915
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xs5
  • Surface level: 0.0915
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5xs5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6752.map.gz (map file in CCP4 format, 275685 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
410 pix
1.13 Å/pix.
= 462.48 Å
410 pix
1.13 Å/pix.
= 462.48 Å
410 pix
1.13 Å/pix.
= 462.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density
Contour Level:0.0915 (by author), 0.0915 (movie #1):
Minimum - Maximum-0.20347741 - 0.36940232
Average (Standard dev.)0.00095367606 (0.023493862)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions410410410
Origin000
Limit409409409
Spacing410410410
CellA=B=C: 462.48 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z462.480462.480462.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS410410410
D min/max/mean-0.2030.3690.001

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Supplemental data

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Sample components

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Entire Coxsackievirus A6

EntireName: Coxsackievirus A6 / Number of components: 4

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Component #1: virus, Coxsackievirus A6

VirusName: Coxsackievirus A6 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Coxsackievirus A6
Shell #1Name of element: Coxsackievirus A6 procapsid particle capsid
T number(triangulation number): 1

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Component #2: protein, Genome polyprotein

ProteinName: Genome polyprotein / Recombinant expression: No
MassTheoretical: 33.467273 kDa
SourceSpecies: Coxsackievirus A6 / Strain: TW-2007-00141

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Component #3: protein, Genome polyprotein

ProteinName: Genome polyprotein / Recombinant expression: No
MassTheoretical: 35.63873 kDa
SourceSpecies: Coxsackievirus A6 / Strain: TW-2007-00141
Source (natural)Organ or tissue: muscle

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Component #4: protein, Genome polyprotein

ProteinName: Genome polyprotein / Recombinant expression: No
MassTheoretical: 26.274836 kDa
SourceSpecies: Coxsackievirus A6
Source (natural)Organ or tissue: muscle

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: NaCl 137mmol/L, KCl 2.7mmol/L, Na2HPO4 10mmol/L, KH2PO4 2mmol/L
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 93000 X (nominal) / Cs: 2.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 312

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 10749
3D reconstructionSoftware: Relion / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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