[English] 日本語
- EMDB-6702: Cryo-EM Study of an Engineered Enterovirus 71-Like Particle Mimic... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 6702
TitleCryo-EM Study of an Engineered Enterovirus 71-Like Particle Mimicking 80S Empty Capsid
SampleEnterovirus A71
SourceEnterovirus A71 / virus
Map data
Methodsingle particle (icosahedral) reconstruction, at 3.71 Å resolution
AuthorsWang X / Ku Z / Zhang X / Cong Y / Huang Z
CitationJ. Virol., 2018, 92

J. Virol., 2018, 92 Yorodumi Papers
Structure, Immunogenicity, and Protective Mechanism of an Engineered Enterovirus 71-Like Particle Vaccine Mimicking 80S Empty Capsid.
Xiaoli Wang / Zhiqiang Ku / Xiang Zhang / Xiaohua Ye / Jinhuan Chen / Qingwei Liu / Wei Zhang / Chao Zhang / Zhenglin Fu / Xia Jin / Yao Cong / Zhong Huang

DateDeposition: Feb 8, 2017 / Header (metadata) release: Oct 18, 2017 / Map release: Oct 25, 2017 / Last update: Nov 1, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_6702.map.gz (map file in CCP4 format, 322487 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
432 pix
1 Å/pix.
= 430.92 Å
432 pix
1 Å/pix.
= 430.92 Å
432 pix
1 Å/pix.
= 430.92 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.9975 Å
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-7.170642 - 13.352638
Average (Standard dev.)2.773026E-9 (1)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 430.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.99750.99750.9975
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z430.920430.920430.920
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-216-216-216
D min/max/mean-7.17113.3530.000

Supplemental data

Sample components

Entire Enterovirus A71

EntireName: Enterovirus A71 / Number of components: 1

Component #1: virus, Enterovirus A71

VirusName: Enterovirus A71 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Enterovirus A71 / virus
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Fall armyworm
Vector: pIEX/Bac-1

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 7887
3D reconstructionResolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more