[English] 日本語
Yorodumi
- EMDB-1004: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1004
TitleRibosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Map data70S ribosome stalled by the antibiotic kirromycin
Sample
  • Sample: Kirromycin stalled 70S Ribosome from E.coli
  • Complex: 70S Ribosome
  • Ligand: EF-Tu, tRNA, GTP
  • RNA: formyl-methionyl tRNA
Function / homology
Function and homology information


misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation ...misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein S13, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S13-like, H2TH / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS13 / Elongation factor Tu / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsStark H / Rodnina MV / Wieden HJ / Zemlin F / Wintermeyer W / van Heel M
CitationJournal: Nat Struct Biol / Year: 2002
Title: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Authors: Holger Stark / Marina V Rodnina / Hans-Joachim Wieden / Friedrich Zemlin / Wolfgang Wintermeyer / Marin van Heel /
Abstract: The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional ...The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.
History
DepositionAug 27, 2002-
Header (metadata) releaseAug 29, 2002-
Map releaseAug 29, 2003-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1004.gif

Downloads & links

-
Map

FileDownload / File: emd_1004.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S ribosome stalled by the antibiotic kirromycin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.25 Å/pix.
x 160 pix.
= 360. Å		2.25 Å/pix.
x 160 pix.
= 360. Å		2.25 Å/pix.
x 160 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.25 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0411 / Movie #1: 0.02
Minimum - Maximum-0.480909 - 0.774331
Average (Standard dev.)0.00151584 (±0.0461972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 360 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.252.252.25
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.4810.7740.002

-
Supplemental data

-
Sample components

-
Entire : Kirromycin stalled 70S Ribosome from E.coli

EntireName: Kirromycin stalled 70S Ribosome from E.coli
Components
  • Sample: Kirromycin stalled 70S Ribosome from E.coli
  • Complex: 70S Ribosome
  • Ligand: EF-Tu, tRNA, GTP
  • RNA: formyl-methionyl tRNA

-
Supramolecule #1000: Kirromycin stalled 70S Ribosome from E.coli

SupramoleculeName: Kirromycin stalled 70S Ribosome from E.coli / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 3
Molecular weightExperimental: 2.5 MDa / Theoretical: 2.5 MDa

-
Supramolecule #1: 70S Ribosome

SupramoleculeName: 70S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

-
Macromolecule #1: EF-Tu, tRNA, GTP

MacromoleculeName: EF-Tu, tRNA, GTP / type: ligand / ID: 1 / Name.synonym: Ternary Complex / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64 KDa

-
Macromolecule #2: formyl-methionyl tRNA

MacromoleculeName: formyl-methionyl tRNA / type: rna / ID: 2 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.07 mg/mL
BufferpH: 7.5
Details: 50mM Tris-HCl, 70mM NH4Cl, 30mM KCl, 7mM MgCl2, 1mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 40 %

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/SOPHIE
TemperatureMin: 4.2 K / Max: 4.2 K / Average: 4.2 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PATCHWORK DENSITOMETER / Digitization - Sampling interval: 13.2 µm / Average electron dose: 15 e/Å2 / Od range: 1.3 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.35 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder: side entry / Specimen holder model: HOME BUILD

-
Image processing

CTF correctionDetails: phase flip
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Imagic / Number images used: 24000

-
Atomic model buiding 1

SoftwareName: Situs and Amira
DetailsProtocol: rigid body. The domains of EF-Tu were fitted seperately by visual docking using O and Swiss PDB viewer
RefinementProtocol: RIGID BODY FIT
Output model

PDB-1mj1:
FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME

+
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