[English] 日本語
Yorodumi
- EMDB-1128: Mechanism for the disassembly of the posttermination complex infe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1128
TitleMechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Map dataThis is a 70S.tRNA(Ile).mRNA.puromycin.RRF complex from E.coli
Sample
  • Sample: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome
  • Complex: 70S
  • Protein or peptide: RRF
  • RNA: tRNA-ILE
  • Other: mRNA
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / cytosol / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein S12, bacterial-type / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.1 Å
AuthorsGao N / Zavialov AV / Li W / Sengupta J / Valle M / Gursky RP / Ehrenberg M / Frank J
CitationJournal: Mol Cell / Year: 2005
Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In ...Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G.
History
DepositionMay 11, 2005-
Header (metadata) releaseMay 11, 2005-
Map releaseMay 11, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1zn1
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1zn0
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1zn1
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1128.gif

Downloads & links

-
Map

FileDownload / File: emd_1128.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 70S.tRNA(Ile).mRNA.puromycin.RRF complex from E.coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 59.600000000000001 / Movie #1: 50
Minimum - Maximum-104.998999999999995 - 275.617999999999995
Average (Standard dev.)5.22223 (±26.999099999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 366.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-104.999275.6185.222

-
Supplemental data

-
Sample components

-
Entire : 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome

EntireName: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome
Components
  • Sample: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome
  • Complex: 70S
  • Protein or peptide: RRF
  • RNA: tRNA-ILE
  • Other: mRNA

-
Supramolecule #1000: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome

SupramoleculeName: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome / type: sample / ID: 1000 / Number unique components: 4

-
Supramolecule #1: 70S

SupramoleculeName: 70S / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL

-
Macromolecule #1: RRF

MacromoleculeName: RRF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No

-
Macromolecule #2: tRNA-ILE

MacromoleculeName: tRNA-ILE / type: rna / ID: 2 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E.coli

-
Macromolecule #3: mRNA

MacromoleculeName: mRNA / type: other / ID: 3 / Classification: DNA/RNA / Structure: SINGLE STRANDED / Synthetic?: Yes

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: polymix buffer
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Quantifoil holley carbon film grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: two-sided blotting plunger
Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 93 K
DateFeb 1, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 15 e/Å2 / Od range: 1.2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Amplitude correction was applied using low-angle x-ray scattering data.
Number images used: 37379

+
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