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

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Basic information

Database: EMDB / ID: EMD-9652
TitleAsymmetrical reconstruction of CVA10 A-particle
Map data
SampleCoxsackievirus A10:
Biological speciesCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / Resolution: 12 Å
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 /
Abstract: Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, ...Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, utilizing the molecule KREMEN1 as an entry receptor, constitutes a KREMEN1-dependent subgroup within HEV-As. Currently, there is no vaccine or antiviral therapy available for treating diseases caused by CVA10. The atomic-resolution structure of the CVA10 virion, which is within the KREMEN1-dependent subgroup, shows significant conformational differences in the putative receptor binding sites and serotype-specific epitopes, when compared to the SCARB2-dependent subgroup of HEV-A, such as EV71, highlighting specific differences between the sub-groups. We also report two expanded structures of CVA10, an empty particle and uncoating intermediate at atomic resolution, as well as a medium-resolution genome structure reconstructed using a symmetry-mismatch method. Structural comparisons coupled with previous results, reveal an ordered signal transmission process for enterovirus uncoating, converting exo-genetic receptor-attachment inputs into a generic RNA release mechanism.
DepositionSep 10, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 16, 2019-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: PDBj / Status: Released

Structure visualization

  • 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:
Supplemental images

Downloads & links


FileDownload / File: emd_9652.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å
1.35 Å/pix.
x 360 pix.
= 486. Å
1.35 Å/pix.
x 360 pix.
= 486. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-7.6655083 - 15.213524
Average (Standard dev.)0.17075863 (±1.711256)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

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

Supplemental data

Sample components

Entire Coxsackievirus A10

EntireName: Coxsackievirus A10 / Number of components: 1

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)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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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