[English] 日本語
Yorodumi
- EMDB-1312: Scaffolding as an organizing principle in trans-translation. The ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1312
TitleScaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Map dataCryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the absence of S1 in solution.
Sample
  • Sample: Thermus thermophilus 70S ribosome
  • Complex: 70S RibosomeRibosome
  • Protein or peptide: small protein B
  • Protein or peptide: EF-Tu
  • RNA: tmRNATransfer-messenger RNA
  • RNA: tRNATransfer RNA
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 13.1 Å
AuthorsGillet R / Kaur S / Li W / Hallier M / Felden B / Frank J
CitationJournal: J Biol Chem / Year: 2007
Title: Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Authors: Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank /
Abstract: A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer- ...A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger RNA, small protein B, and ribosome protein S1. By means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein B, which appears near the decoding center. This result suggests that, when lacking a codon, the A-site on the small subunit is a target for small protein B. To investigate the role of S1 played in trans-translation, we obtained a cryo-electron microscopic map, including a stalled ribosome, transfer-messenger RNA, and small protein Bs but in the absence of S1. In this complex, several connections between the 30 S subunit and transfer-messenger RNA that appear in the +S1 complex are no longer found. We propose the unifying concept of scaffolding for the roles of small protein B and S1 in binding of transfer-messenger RNA to the ribosome during trans-translation, and we infer a pathway of sequential binding events in the initial phase of trans-translation.
History
DepositionDec 13, 2006-
Header (metadata) releaseDec 14, 2006-
Map releaseDec 14, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1312.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Thermus thermophilus 70S ribosome bound with tmRNA, two small protein B, and EF-Tu in the absence of S1 in solution.
Voxel sizeX=Y=Z: 2.82 Å
Density
Contour Level1: 71.5 / Movie #1: 40
Minimum - Maximum-113.409999999999997 - 310.201000000000022
Average (Standard dev.)5.60667 (±30.110299999999999)
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-63-63-63
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-113.410310.2015.607

-
Supplemental data

-
Sample components

-
Entire : Thermus thermophilus 70S ribosome

EntireName: Thermus thermophilus 70S ribosome
Components
  • Sample: Thermus thermophilus 70S ribosome
  • Complex: 70S RibosomeRibosome
  • Protein or peptide: small protein B
  • Protein or peptide: EF-Tu
  • RNA: tmRNATransfer-messenger RNA
  • RNA: tRNATransfer RNA

-
Supramolecule #1000: Thermus thermophilus 70S ribosome

SupramoleculeName: Thermus thermophilus 70S ribosome / type: sample / ID: 1000 / Number unique components: 5
Molecular weightExperimental: 2.4 MDa

-
Supramolecule #1: 70S Ribosome

SupramoleculeName: 70S Ribosome / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL
Molecular weightTheoretical: 2.3 MDa

-
Macromolecule #1: small protein B

MacromoleculeName: small protein B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 19 KDa

-
Macromolecule #4: EF-Tu

MacromoleculeName: EF-Tu / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Thermus thermophilus (bacteria)

-
Macromolecule #2: tmRNA

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

-
Macromolecule #3: tRNA

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

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: see Methods
StainingType: NEGATIVE / Details: No staining (Cryo-EM)
GridDetails: Quanti-foil grids coated with a thin carbon layer
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 279 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blot for 5 seconds before plunging Rapid plunge freezing in liquid ethane

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.244 µm / Nominal defocus min: 1.703 µm / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateAug 21, 2004
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 42 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: CTF correctionn of 3D map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 31731

-
Atomic model buiding 1

SoftwareName: O
DetailsProtocol: Rigid Body. manual fitting with O
RefinementProtocol: RIGID BODY 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