[English] 日本語
Yorodumi
- PDB-4crn: Cryo-EM of a pretermination complex with eRF1 and eRF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4crn
TitleCryo-EM of a pretermination complex with eRF1 and eRF3
Components
  • ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX
  • ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX
KeywordsTRANSLATION / TERMINATION / CRYO-EM
Function / homology
Function and homology information


Eukaryotic Translation Termination / sno(s)RNA transcription / translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Eukaryotic Translation Termination / sno(s)RNA transcription / translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / DNA-templated transcription termination / cytoplasmic stress granule / regulation of translation / ribosome binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / mRNA binding / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 ...Eukaryotic peptide chain release factor GTP-binding subunit / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / : / GTP-eEF1A C-terminal domain-like / : / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Eukaryotic peptide chain release factor GTP-binding subunit / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsPreis, A. / Heuer, A. / Barrio-Garcia, C. / Hauser, A. / Eyler, D. / Berninghausen, O. / Green, R. / Becker, T. / Beckmann, R.
CitationJournal: Cell Rep / Year: 2014
Title: Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1.
Authors: Anne Preis / Andre Heuer / Clara Barrio-Garcia / Andreas Hauser / Daniel E Eyler / Otto Berninghausen / Rachel Green / Thomas Becker / Roland Beckmann /
Abstract: Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and ...Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and guanosine triphosphate (GTP)-bound eRF3. After GTP hydrolysis, eRF3 dissociates, and ABCE1 can bind to eRF1-loaded ribosomes to stimulate peptide release and ribosomal subunit dissociation. Here, we present cryoelectron microscopic (cryo-EM) structures of a pretermination complex containing eRF1-eRF3 and a termination/prerecycling complex containing eRF1-ABCE1. eRF1 undergoes drastic conformational changes: its central domain harboring the catalytically important GGQ loop is either packed against eRF3 or swung toward the peptidyl transferase center when bound to ABCE1. Additionally, in complex with eRF3, the N-terminal domain of eRF1 positions the conserved NIKS motif proximal to the stop codon, supporting its suggested role in decoding, yet it appears to be delocalized in the presence of ABCE1. These results suggest that stop codon decoding and peptide release can be uncoupled during termination.
History
DepositionFeb 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Structure summary
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2597
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2597
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2597
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX
X: ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3963
Polymers96,8732
Non-polymers5221
Water00
1


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

-
Components

#1: Protein ERF3 IN RIBOSOME BOUND ERF1-ERF3-GDPNP COMPLEX


Mass: 47840.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN P (ERF3) THE FIRST 254 AMINO ACIDS ARE MISSING.
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTYB2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05453
#2: Protein ERF1 IN RIBOSOME-BOUND ERF1-ERF3-GDPNP COMPLEX


Mass: 49032.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN X THE LAST 25 AMINO ACIDS (416-440) ARE MISSING
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTYB2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12385
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Sequence detailsTHE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS ...THE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS (RESIDUES 416-440) ARE MISSING IN THE MODEL

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: CMV-STALLED WHEAT GERM 80S-RNC BOUND TO ERF1 AND ABCE1-ADPNP
Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE, VITROBOT MARK 4

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 20, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 147136 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 0.02 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)

-
Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3STARFISHparticle selection
4SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 9.1 Å / Num. of particles: 39309
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2597 (DEPOSITION ID: 12368).
Symmetry type: POINT
RefinementHighest resolution: 9.1 Å
Refinement stepCycle: LAST / Highest resolution: 9.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 32 0 6693

+
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