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- EMDB-6829: Cryo-EM Structure of CVA6 VLP -

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Basic information

Database: EMDB / ID: 6829
TitleCryo-EM Structure of CVA6 VLP
SampleCoxsackievirus A6
SourceCoxsackievirus A6 / virus
Map data
Methodsingle particle reconstruction, at 3 Å resolution
AuthorsChen J / Zhang C
CitationJ. Virol., 2018, 92

J. Virol., 2018, 92 Yorodumi Papers
A 3.0-Angstrom Resolution Cryo-Electron Microscopy Structure and Antigenic Sites of Coxsackievirus A6-Like Particles.
Jinhuan Chen / Chao Zhang / Yu Zhou / Xiang Zhang / Chaoyun Shen / Xiaohua Ye / Wen Jiang / Zhong Huang / Yao Cong

Validation ReportPDB-ID: 5yhq

SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Nov 1, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5yhq
  • Surface level: 1.8
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5yhq
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_6829.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
0.82 Å/pix.
= 393.6 Å
480 pix
0.82 Å/pix.
= 393.6 Å
480 pix
0.82 Å/pix.
= 393.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.82 Å
Contour Level:1.8 (by author), 1.8 (movie #1):
Minimum - Maximum-8.361276 - 15.031386
Average (Standard dev.)1.6683748E-6 (0.9999974)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 393.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-240-240-240
D min/max/mean-8.36115.0310.000

Supplemental data

Sample components

Entire Coxsackievirus A6

EntireName: Coxsackievirus A6 / Number of components: 4

Component #1: virus, Coxsackievirus A6

VirusName: Coxsackievirus A6 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Coxsackievirus A6 / virus
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Fall armyworm

Component #2: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Recombinant expression: No
MassTheoretical: 33.644395 kDa
Source (engineered)Expression System: Coxsackievirus A6 / virus

Component #3: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Recombinant expression: No
MassTheoretical: 26.375834 kDa
Source (engineered)Expression System: Coxsackievirus A6 / virus

Component #4: protein, capsid protein VP0

ProteinName: capsid protein VP0 / Recombinant expression: No
MassTheoretical: 35.351426 kDa
Source (engineered)Expression System: Coxsackievirus A6 / virus

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE

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: 42 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 11596
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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