[English] 日本語
- EMDB-6712: Inner capsid of Rice Dwarf Virus -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 6712
TitleInner capsid of Rice Dwarf Virus
Map data
SampleRice dwarf virus (isolate O):
virus / Core protein P3
SourceRice dwarf virus (isolate O)
Methodsingle particle reconstruction / cryo EM / 13.43 Å resolution
AuthorsNakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Murata K / Nakagawa A
CitationJournal: To be published
Title: The second layer shell assembly mechanism of multi-layerd Reoviridae
Authors: Nakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Narita H / Shimizu T / Uehara-Ichiki T / Omura T / Murata K / Nakagawa A
DateDeposition: Mar 14, 2017 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0403
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0403
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_6712.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
1.88 Å/pix.
= 658. Å
350 pix
1.88 Å/pix.
= 658. Å
350 pix
1.88 Å/pix.
= 658. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Contour Level:0.0403 (by author), 0.0403 (movie #1):
Minimum - Maximum-0.005345597 - 0.118807636
Average (Standard dev.)0.014704836 (0.021045744)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 658.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.881.881.88
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z658.000658.000658.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0050.1190.015

Supplemental data

Sample components

Entire Rice dwarf virus (isolate O)

EntireName: Rice dwarf virus (isolate O) / Number of components: 2

Component #1: virus, Rice dwarf virus (isolate O)

VirusName: Rice dwarf virus (isolate O) / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Rice dwarf virus (isolate O)
Shell #1Name of element: inner shell capsid / T number(triangulation number): 1

Component #2: protein, Core protein P3

ProteinName: Core protein P3 / Recombinant expression: No
SourceSpecies: Rice dwarf virus (isolate O)

Experimental details

Sample preparation

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

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 4.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: omega / Energy window: 0-20 eV
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 784
3D reconstructionResolution: 13.43 Å / Resolution method: FSC 0.143 CUT-OFF

About Yorodumi


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

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

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more