[English] 日本語
Yorodumi
- EMDB-2691: Inside rotavirus at 7 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2691
TitleInside rotavirus at 7 A resolution
Map datalow-pass filtered map (10A) for dsRNA visualization
Sample
  • Sample: Rotavirus DLP+VP1
  • Protein or peptide: Rotavirus polymerase (VP1)
  • RNA: dsRNARNA
Keywordsrotavirus / dsRNA-dependent / polymerase / dsRNA / symmetry-mismatch / VP1
Biological speciesBovine rotavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsEstrozi LF
CitationJournal: To Be Published
Title: Inside rotavirus at 7 A resolution
Authors: Estrozi LF
History
DepositionJun 23, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 15, 2015-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2691.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlow-pass filtered map (10A) for dsRNA visualization
Voxel sizeX=Y=Z: 1.98413 Å
Density
Contour LevelBy EMDB: 0.4 / Movie #1: 2
Minimum - Maximum-12.44486904 - 12.18700218
Average (Standard dev.)-0.00000698 (±0.92164183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-91-91-56
Dimensions183183184
Spacing183183184
CellA: 363.0958 Å / B: 363.0958 Å / C: 365.07993 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9841311475411.9841311475411.9841304347826
M x/y/z183183184
origin x/y/z0.0000.0000.000
length x/y/z363.096363.096365.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-91-91-56
NC/NR/NS183183184
D min/max/mean-12.44512.187-0.000

-
Supplemental data

-
Sample components

-
Entire : Rotavirus DLP+VP1

EntireName: Rotavirus DLP+VP1
Components
  • Sample: Rotavirus DLP+VP1
  • Protein or peptide: Rotavirus polymerase (VP1)
  • RNA: dsRNARNA

-
Supramolecule #1000: Rotavirus DLP+VP1

SupramoleculeName: Rotavirus DLP+VP1 / type: sample / ID: 1000 / Oligomeric state: VP1 and dsRNA molecules / Number unique components: 2

-
Macromolecule #1: Rotavirus polymerase (VP1)

MacromoleculeName: Rotavirus polymerase (VP1) / type: protein_or_peptide / ID: 1 / Name.synonym: VP1
Details: The icosahedral 3D reconstruction of rotavirus DLP shows extra-density near the 5-fold axis corresponding to one copy of VP1 attached to the DLP inner surface.
Number of copies: 11 / Recombinant expression: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus
Molecular weightTheoretical: 126.326 KDa

-
Macromolecule #2: dsRNA

MacromoleculeName: dsRNA / type: rna / ID: 2 / Name.synonym: dsRNA / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridDetails: Lacy carbon and C-flat
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature
Method: Blot for 3 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56540 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric, side-entry / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected
DateJun 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 11289 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase-flipping
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Imagic, RIco, bsoft, ctffind3, FPM / Number images used: 11289

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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