[English] 日本語
- EMDB-8108: Structure of RelA bound to the 70S ribosome (overall map, class 2) -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 8108
TitleStructure of RelA bound to the 70S ribosome (overall map, class 2)
Map data
Sample70 S ribosome:
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 3 Å resolution
AuthorsBrown A / Fernandez IS / Gordiyenko Y / Ramakrishnan V
CitationJournal: Nature / Year: 2016
Title: Ribosome-dependent activation of stringent control.
Authors: Alan Brown / Israel S Fernández / Yuliya Gordiyenko / V Ramakrishnan
DateDeposition: Mar 11, 2016 / Header (metadata) release: Jun 29, 2016 / Map release: Jun 29, 2016 / Last update: Jul 12, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_8108.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.6347005 - 1.1297468
Average (Standard dev.)0.0014723118 (0.025488678)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 536.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
start NX/NY/NZ00-41
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.6351.1300.001

Supplemental data

Sample components

Entire 70 S ribosome

EntireName: 70 S ribosome / Number of components: 1

Component #1: protein, 70 S ribosome

ProteinName: 70 S ribosome / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Grids were blotted for 5 s.

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 104478.0 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1800.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

Image acquisition

Image acquisitionDetails: FEI Falcon III Images were collected in movie-mode at 30 frames per second

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 98498
3D reconstructionSoftware: RELION / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

Atomic model buiding

Modeling #1Target criteria: Average FSC / Refinement space: RECIPROCAL
Input PDB model: 4YBB
Overall bvalue: 112.700000000000003

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. 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

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