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- EMDB-9652: Asymmetrical reconstruction of CVA10 A-particle -

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Basic information

Entry
Database: EMDB / ID: 9652
TitleAsymmetrical reconstruction of CVA10 A-particle
Map data
SampleCoxsackievirus A10:
virus
SourceCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / 12 Å resolution
AuthorsZhu L / Sun Y / Rao ZH / Wang XX
CitationJournal: Nat Commun / Year: 2018
Title: Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating.
Authors: Ling Zhu / Yao Sun / Jinyan Fan / Bin Zhu / Lei Cao / Qiang Gao / Yanjun Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang
DateDeposition: Sep 10, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9652.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/pix.
= 486. 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
Contour Level:5.5 (by author), 5.5 (movie #1):
Minimum - Maximum-7.6655083 - 15.213524
Average (Standard dev.)0.17075863 (1.711256)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin-267.0-267.0-267.0
Limit92.092.092.0
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-267-267-267
NC/NR/NS360360360
D min/max/mean-7.66615.2140.171

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Supplemental data

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Sample components

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Entire Coxsackievirus A10

EntireName: Coxsackievirus A10 / Number of components: 1

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Component #1: virus, Coxsackievirus A10

VirusName: Coxsackievirus A10 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
SpeciesSpecies: Coxsackievirus A10
Source (engineered)Expression System: Chlorocebus aethiops (grivet)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 6500
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF

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