[English] 日本語
Yorodumi
- EMDB-1071: Three-dimensional structures of translating ribosomes by Cryo-EM. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1071
TitleThree-dimensional structures of translating ribosomes by Cryo-EM.
Map data3D reconstruction of an E. coli ribosome stalled in translation of tandem immunoglobulin domains from the Actin Binding Protein of Distyostelium disocideum.
Sample
  • Sample: E. coli ribosome translating 2 Ig domains
  • Complex: E. coli 30S subunit
  • Complex: E. coli 50S subunit
  • RNA: P site tRNA
  • RNA: E site tRNA
  • Protein or peptide: Tandem Ig domains of D. discoideum ABP
Biological speciesEscherichia coli (E. coli) / Dictyostelium discoideum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.2 Å
AuthorsGilbert RJC / Fucini P / Connell S / Fuller SD / Nierhaus KH / Robinson CV / Dobson CM / Stuart DI
CitationJournal: Mol Cell / Year: 2004
Title: Three-dimensional structures of translating ribosomes by Cryo-EM.
Authors: Robert J C Gilbert / Paola Fucini / Sean Connell / Stephen D Fuller / Knud H Nierhaus / Carol V Robinson / Christopher M Dobson / David I Stuart /
Abstract: Cryo-electron microscopy and image reconstruction techniques have been used to obtain three-dimensional maps for E. coli ribosomes stalled following translation of three representative proteins. ...Cryo-electron microscopy and image reconstruction techniques have been used to obtain three-dimensional maps for E. coli ribosomes stalled following translation of three representative proteins. Comparisons of these electron density maps, at resolutions of between 13 and 16 A, with that of a nontranslating ribosome pinpoint specific structural differences in stalled ribosomes and identify additional material, including tRNAs and mRNA. In addition, the tunnel through the large subunit, the anticipated exit route of newly synthesized proteins, is partially occluded in all the stalled ribosome structures. This observation suggests that significant segments of the nascent polypeptide chains examined here could be located within an expanded tunnel, perhaps in a rudimentary globular conformation. Such behavior could be an important aspect of the folding of at least some proteins in the cellular environment.
History
DepositionMar 14, 2004-
Header (metadata) releaseMar 14, 2004-
Map releaseApr 28, 2004-
UpdateDec 10, 2014-
Current statusDec 10, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.95170116
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.952
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1071.gif

Downloads & links

-
Map

FileDownload / File: emd_1071.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of an E. coli ribosome stalled in translation of tandem immunoglobulin domains from the Actin Binding Protein of Distyostelium disocideum.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
3.33 Å/pix.
x 128 pix.
= 426.24 Å		3.33 Å/pix.
x 128 pix.
= 426.24 Å		3.33 Å/pix.
x 128 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.33 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.03 / Movie #1: 0.9517012
Minimum - Maximum-2.25436 - 2.90426
Average (Standard dev.)-0.0101516 (±0.414727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 426.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.333.333.33
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z426.240426.240426.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128128
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-2.2542.904-0.010

-
Supplemental data

-
Sample components

-
Entire : E. coli ribosome translating 2 Ig domains

EntireName: E. coli ribosome translating 2 Ig domains
Components
  • Sample: E. coli ribosome translating 2 Ig domains
  • Complex: E. coli 30S subunit
  • Complex: E. coli 50S subunit
  • RNA: P site tRNA
  • RNA: E site tRNA
  • Protein or peptide: Tandem Ig domains of D. discoideum ABP

-
Supramolecule #1000: E. coli ribosome translating 2 Ig domains

SupramoleculeName: E. coli ribosome translating 2 Ig domains / type: sample / ID: 1000 / Details: The sample was monodisperse.
Oligomeric state: 30S subunit and 50S subunit, 2 tRNA molecules, 1 nascent protein and 1 Ig nascent polypeptide
Number unique components: 5

-
Supramolecule #1: E. coli 30S subunit

SupramoleculeName: E. coli 30S subunit / type: complex / ID: 1 / Name.synonym: 30S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #2: E. coli 50S subunit

SupramoleculeName: E. coli 50S subunit / type: complex / ID: 2 / Name.synonym: 50S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: P site tRNA

MacromoleculeName: P site tRNA / type: rna / ID: 1 / Details: partial occupancy / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #2: E site tRNA

MacromoleculeName: E site tRNA / type: rna / ID: 2 / Details: partial occupancy lower than P site / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #3: Tandem Ig domains of D. discoideum ABP

MacromoleculeName: Tandem Ig domains of D. discoideum ABP / type: protein_or_peptide / ID: 3 / Name.synonym: Ig2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Dictyostelium discoideum (eukaryote) / synonym: Slime mould
Recombinant expressionOrganism: In vitro transcription.translation system / Recombinant plasmid: pT7-7

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.0 mg/mL
BufferDetails: 20 mM HEPES, 150 mM ammonium acetate, 6 mM magnesium acetate, 2 mM spermidine, 0.05 mM spermine and 4 mM 2-mercaptoethanol. Concentration of ribosomes expressed to A260 units.
GridDetails: 300 mesh copper grid with holey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Standard unmodified guillotine plunger

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
DateMay 1, 2000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 8.322 µm / Number real images: 14 / Od range: 5 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2 mm / Nominal defocus max: 3.49 µm / Nominal defocus min: 1.62 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: Each negative dataset
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC, GAP, CNS, XPLOR
Details: Final maps were calculated from 4434 images from a total of 8898 from 14 individual datasets, with scaling in reciprocal space to crystallographic ribosome structures and correction for map ...Details: Final maps were calculated from 4434 images from a total of 8898 from 14 individual datasets, with scaling in reciprocal space to crystallographic ribosome structures and correction for map anisotropy by B-factor weighting of amplitudes in XPLOR with respect to a similarly-treated control inactive ribosome. Selection of particles for inclusion in the final maps was by correlation coefficient with respect to the alignment model, designed to maximise nascent chain occupancy in the selected images.
Number images used: 4434
Final angle assignmentDetails: SPIDER euler

-
Atomic model buiding 1

SoftwareName: GAP
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor and correlation coefficient

+
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