[English] 日本語
Yorodumi
- EMDB-1110: Structural basis for the function of the ribosomal L7/12 stalk in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1110
TitleStructural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
Map dataThis is a map of the E.coli Ribosome in complex with elongation factor G in the presence of the antibiotic fusidic acid.
Sample
  • Sample: E coli ribosome in complex with elongation factor G
  • Complex: 70S
  • Protein or peptide: Elongation Factor GEF-G
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsDiaconu M / Kothe U / Schlunzen F / Harms JM / Fischer N / Stark H / Rodnina MV / Wahl MC
CitationJournal: Cell / Year: 2005
Title: Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
Authors: Mihaela Diaconu / Ute Kothe / Frank Schlünzen / Niels Fischer / Jörg M Harms / Alexander G Tonevitsky / Holger Stark / Marina V Rodnina / Markus C Wahl /
Abstract: The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 ...The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify these elements in cryo-electron-microscopic reconstructions of Escherichia coli ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers in T. maritima and two in E. coli, in concordance with the different length of helix alpha8 of L10 in these organisms. The stalk is organized into three elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation.
History
DepositionFeb 22, 2005-
Header (metadata) releaseFeb 23, 2005-
Map releaseJul 5, 2005-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.242957435
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.242957435
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1110.gif

Downloads & links

-
Map

FileDownload / File: emd_1110.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the E.coli Ribosome in complex with elongation factor G in the presence of the antibiotic fusidic acid.
Voxel sizeX=Y=Z: 3.2 Å
Density
Contour Level1: 0.188 / Movie #1: 0.2429574
Minimum - Maximum-0.763816 - 0.820372
Average (Standard dev.)0.00090719 (±0.111531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions108108108
Spacing108108108
CellA=B=C: 345.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.23.23.2
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-80-80-80
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
D min/max/mean-0.7640.8200.001

-
Supplemental data

-
Sample components

-
Entire : E coli ribosome in complex with elongation factor G

EntireName: E coli ribosome in complex with elongation factor G
Components
  • Sample: E coli ribosome in complex with elongation factor G
  • Complex: 70S
  • Protein or peptide: Elongation Factor GEF-G

-
Supramolecule #1000: E coli ribosome in complex with elongation factor G

SupramoleculeName: E coli ribosome in complex with elongation factor G / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 2.5 MDa

-
Supramolecule #1: 70S

SupramoleculeName: 70S / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

-
Macromolecule #1: Elongation Factor G

MacromoleculeName: Elongation Factor G / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.0 mg/mL
BufferpH: 7.5
Details: 50 mM Tris HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made / Method: Blotted manually for two seconds before plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.0 µm / Number real images: 12 / Average electron dose: 15 e/Å2 / Od range: 1.3 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 8000
DetailsThe particles were selected manually.

-
Atomic model buiding 1

SoftwareName: Amira 3.1, TGS Software
DetailsProtocol: Rigid Body. Manual fitting
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