[English] 日本語
Yorodumi
- EMDB-2373: ribosome-RelA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2373
Titleribosome-RelA complex
Map datareconstruction of ribosome-RelA complex
Sample
  • Sample: 70S-RelA complex
  • Complex: 70S ribosome
  • RNA: deacylated tRNA
  • RNA: tRNA
  • RNA: tRNA
  • Protein or peptide: RelA
Keywordsribosome / RelA / stringent response
Biological speciesThermus thermophilus (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.5 Å
AuthorsAgirrezabala X / Fernandez I / Kelley A / Gil-Carton D / Ramakrishnan V / Valle M
CitationJournal: EMBO Rep / Year: 2013
Title: The ribosome triggers the stringent response by RelA via a highly distorted tRNA.
Authors: Xabier Agirrezabala / Israel S Fernández / Ann C Kelley / David Gil Cartón / Venki Ramakrishnan / Mikel Valle /
Abstract: The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated ...The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated tRNA in the ribosome as a symptom of amino-acid starvation to synthesize the alarmone (p)ppGpp. Here we report a cryo-EM study of RelA bound to ribosomes bearing cognate, deacylated tRNA in the A-site. The data show that RelA on the ribosome stabilizes an unusual distorted form of the tRNA, with the acceptor arm making contact with RelA and far from its normal location in the peptidyl transferase centre.
History
DepositionMay 14, 2013-
Header (metadata) releaseMay 29, 2013-
Map releaseJul 31, 2013-
UpdateSep 11, 2013-
Current statusSep 11, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.175
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.175
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2373-4.tif

Downloads & links

-
Map

FileDownload / File: emd_2373.map.gz / Format: CCP4 / Size: 34.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of ribosome-RelA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 210 pix.
= 367.5 Å		1.75 Å/pix.
x 210 pix.
= 367.5 Å		1.75 Å/pix.
x 210 pix.
= 367.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175 / Movie #1: 0.175
Minimum - Maximum-0.22494394 - 1.17451715
Average (Standard dev.)0.0393284 (±0.15456907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 367.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z367.500367.500367.500
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.2251.1750.039

-
Supplemental data

-
Sample components

-
Entire : 70S-RelA complex

EntireName: 70S-RelA complex
Components
  • Sample: 70S-RelA complex
  • Complex: 70S ribosome
  • RNA: deacylated tRNA
  • RNA: tRNA
  • RNA: tRNA
  • Protein or peptide: RelA

-
Supramolecule #1000: 70S-RelA complex

SupramoleculeName: 70S-RelA complex / type: sample / ID: 1000 / Number unique components: 5
Molecular weightTheoretical: 2.5 MDa

-
Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 2.5 MDa

-
Macromolecule #1: deacylated tRNA

MacromoleculeName: deacylated tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

-
Macromolecule #2: tRNA

MacromoleculeName: tRNA / type: rna / ID: 2 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

-
Macromolecule #3: tRNA

MacromoleculeName: tRNA / type: rna / ID: 3 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

-
Macromolecule #4: RelA

MacromoleculeName: RelA / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.45
Details: 5mM Hepes-KOH pH 7.45, 50mM KCl, 10mM NH4Cl, 10mM Mg-acetate, 5mM beta-mercapto-ethanol
StainingType: NEGATIVE / Details: cryo
GridDetails: Quantifoil grids (2/4) with thin carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 3 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 2200FS
Alignment procedureLegacy - Astigmatism: corrected at 100k
Specialist opticsEnergy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJan 15, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 425 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

-
Image processing

Detailsparticles were selected by combining automated particle picking , multivariate data analysis and visual inspection
CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP, SPIDER / Number images used: 28791

-
Atomic model buiding 1

Initial modelPDB ID:

2wrn
PDB Unreleased entry

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

-
Atomic model buiding 2

Initial modelPDB ID:

2wro
PDB Unreleased entry

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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