[English] 日本語
Yorodumi
- PDB-1fcw: TRNA POSITIONS DURING THE ELONGATION CYCLE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fcw
TitleTRNA POSITIONS DURING THE ELONGATION CYCLE
ComponentsTRNAPHE
KeywordsRIBOSOME / tRNA binding sites / protein synthesis / elongation cycle
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å
AuthorsAgrawal, R.K. / Spahn, C.M.T. / Penczek, P. / Grassucci, R.A. / Nierhaus, K.H. / Frank, J.
CitationJournal: J Cell Biol / Year: 2000
Title: Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle.
Authors: R K Agrawal / C M Spahn / P Penczek / R A Grassucci / K H Nierhaus / J Frank /
Abstract: Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the ...Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNA(f)(Met)-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon-anticodon interaction at the E site appears feasible.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRNAPHE
B: TRNAPHE
C: TRNAPHE
D: TRNAPHE
E: TRNAPHE


Theoretical massNumber of molelcules
Total (without water)124,4515
Polymers124,4515
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: RNA chain
TRNAPHE


Mass: 24890.121 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: tRNA-Ribosome complex / Type: COMPLEX / Source: MULTIPLE SOURCES
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: other / Details: electron microscopy

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420
Electron gunElectron source: OTHER / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 52200 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM
Image scansScanner model: PERKIN ELMER

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 17 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 15610 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: DETAILS--TRNA COORDINATES (TRNA09) WERE FIT INTO CRYO-EM MAP AS RIGID BODIES THE RELATIVE POSITIONS OF THE TRNA IS DERIVED BY FITTING THE X-RAY STRUCTURE OF TRNA (TRNA09) INTO THE THREE- ...Details: DETAILS--TRNA COORDINATES (TRNA09) WERE FIT INTO CRYO-EM MAP AS RIGID BODIES THE RELATIVE POSITIONS OF THE TRNA IS DERIVED BY FITTING THE X-RAY STRUCTURE OF TRNA (TRNA09) INTO THE THREE-DIMENSIONAL CRYO-ELECTRON MICROSCOPY MAPS OF FUNCTIONAL COMPLEXES OF THE E. COLI 70S RIBOSOMES. IT SHOULD BE NOTED THAT ALL TRNA-BINDING POSITIONS ARE NOT OCCUPIED SIMULTANEOSLY. THEREFORE, THERE ARE OVERLAPS BETWEEN THE TWO TRNA COORDINATES. IN ORDER TO SEE THE RELATIVE POSITIONS OF VARIOUS RIBOSOMAL DOMAINS, CHAIN C (THE P-SITE TRNA) SHOULD BE ALIGNED WITH OUR EARLIER DEPOSITED P-SITE POSITION (ID CODE 1EGO).
RefinementHighest resolution: 17 Å
Refinement stepCycle: LAST / Highest resolution: 17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8260 0 0 8260

+
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