[English] 日本語
Yorodumi
- EMDB-1670: Structure of a rabbit ribosome with P site tRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1670
TitleStructure of a rabbit ribosome with P site tRNA
Map dataThis is a map of a rabbit reticulocyte lysate ribosome stalled on a mRNA by a stem-loop with a P-site tRNA.
Sample
  • Sample: Rabbit reticulocyte ribosome stalled on a stem-loop-containing mRNA with a P-site tRNA
  • Organelle or cellular component: 80S ribosomeEukaryotic ribosome
  • RNA: tRNATransfer RNA
  • RNA: Infectious bronchitis virus mRNA
KeywordsRibosome / mRNA / tRNA / stem-loop
Biological speciesOryctolagus cuniculus (rabbit) / Infectious bronchitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 13.6 Å
AuthorsFlanagan IV JF / Namy O / Brierley I / Gilbert RJC
CitationJournal: Structure / Year: 2010
Title: Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes.
Authors: John F Flanagan / Olivier Namy / Ian Brierley / Robert J C Gilbert /
Abstract: Transfer RNAs (tRNAs) link the genetic code in the form of messenger RNA (mRNA) to protein sequence. Translocation of tRNAs through the ribosome from aminoacyl (A) site to peptidyl (P) site and from ...Transfer RNAs (tRNAs) link the genetic code in the form of messenger RNA (mRNA) to protein sequence. Translocation of tRNAs through the ribosome from aminoacyl (A) site to peptidyl (P) site and from P site to exit site is catalyzed in eukaryotes by the translocase elongation factor 2 (EF-2) and in prokaryotes by its homolog EF-G. During tRNA movement one or more "hybrid" states (A/P) is occupied, but molecular details of them and of the translocation process are limited. Here we show by cryo-electron microscopy that a population of mammalian ribosomes stalled at an mRNA pseudoknot structure contains structurally distorted tRNAs in two different A/P hybrid states. In one (A/P'), the tRNA is in contact with the translocase EF-2, which induces it. In the other (A/P''), the translocase is absent. The existence of these alternative A/P intermediate states has relevance to our understanding of the mechanics and kinetics of translocation.
History
DepositionDec 16, 2009-
Header (metadata) releaseApr 9, 2010-
Map releaseApr 9, 2010-
UpdateApr 9, 2010-
Current statusApr 9, 2010Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1670.gif

Downloads & links

-
Map

FileDownload / File: emd_1670.map.gz / Format: CCP4 / Size: 96.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of a rabbit reticulocyte lysate ribosome stalled on a mRNA by a stem-loop with a P-site tRNA.
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 0.00118 / Movie #1: 0.0025
Minimum - Maximum-0.0131587 - 0.0216875
Average (Standard dev.)0.0000812938 (±0.00116409)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 532.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z532.800532.800532.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-0.0130.0220.000

-
Supplemental data

-
Sample components

-
Entire : Rabbit reticulocyte ribosome stalled on a stem-loop-containing mR...

EntireName: Rabbit reticulocyte ribosome stalled on a stem-loop-containing mRNA with a P-site tRNA
Components
  • Sample: Rabbit reticulocyte ribosome stalled on a stem-loop-containing mRNA with a P-site tRNA
  • Organelle or cellular component: 80S ribosomeEukaryotic ribosome
  • RNA: tRNATransfer RNA
  • RNA: Infectious bronchitis virus mRNA

-
Supramolecule #1000: Rabbit reticulocyte ribosome stalled on a stem-loop-containing mR...

SupramoleculeName: Rabbit reticulocyte ribosome stalled on a stem-loop-containing mRNA with a P-site tRNA
type: sample / ID: 1000 / Oligomeric state: Ribosome, mRNA and tRNA / Number unique components: 3

-
Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Ribosome
Details: Sample was purified by affinity chromatography using a tag in the mRNA.
Number of copies: 1 / Oligomeric state: 40S and 60S / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Reticulocytes

-
Macromolecule #1: tRNA

MacromoleculeName: tRNA / type: rna / ID: 1 / Name.synonym: tRNA
Details: Sample was purified by affinity chromatography using a tag in the mRNA.
Classification: TRANSFER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit

-
Macromolecule #2: Infectious bronchitis virus mRNA

MacromoleculeName: Infectious bronchitis virus mRNA / type: rna / ID: 2 / Name.synonym: mRNA / Details: Sample was purified by affinity chromatography. / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Infectious bronchitis virus

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
Details: 25mM Hepes-KOH pH 7.8, 5mM MgOAc, 1mM cycloheximide, 150mM KOAc
GridDetails: 300 mesh copper grid with lacey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homemade plunger / Method: Blot with Whatman number 1 paper

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 115 K
Alignment procedureLegacy - Astigmatism: At 200,000 magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 65 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Per micrograph
Final angle assignmentDetails: Spider convention
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, WellMAP
Details: Maps were calculated using 24738 out of 38720 particles selected by the P-site tRNA presence. Presence of the tRNA was proved using multivariate statistical analysis focused classification ...Details: Maps were calculated using 24738 out of 38720 particles selected by the P-site tRNA presence. Presence of the tRNA was proved using multivariate statistical analysis focused classification of particles without previous alignment to a tRNA-containing ribosome.
Number images used: 24738

-
Atomic model buiding 1

Initial modelPDB ID:

2zkq
PDB Unreleased entry

SoftwareName: URO
DetailsProtocol: Rigid body in segments. Subregions were defined as described in the paper accompanying this deposition.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

-
Atomic model buiding 2

Initial modelPDB ID:

2zkr
PDB Unreleased entry

SoftwareName: URO
DetailsProtocol: Rigid body in segments. Subregions were defined as described in the paper accompanying this deposition.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: 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