[English] 日本語
Yorodumi
- PDB-2vrh: Structure of the E. coli trigger factor bound to a translating ri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vrh
TitleStructure of the E. coli trigger factor bound to a translating ribosome
Components
  • 50S RIBOSOMAL PROTEIN L23
  • 50S RIBOSOMAL PROTEIN L24
  • 50S RIBOSOMAL PROTEIN L29
  • TRIGGER FACTOR
KeywordsRIBOSOME / TRIGGER FACTOR / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / CO-TRANSLATIONAL PROTEIN FOLDING / ROTAMASE / CHAPERONE / ISOMERASE / CELL CYCLE / RNA-BINDING / RRNA-BINDING / CELL DIVISION / RIBOSOME-NASCENT CHAIN COMPLEX
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal large subunit assembly / protein transport / large ribosomal subunit rRNA binding ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal large subunit assembly / protein transport / large ribosomal subunit rRNA binding / ribosome binding / cytoplasmic translation / cytosolic large ribosomal subunit / response to heat / rRNA binding / ribosome / structural constituent of ribosome / cell cycle / translation / cell division / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L24 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL29 / Trigger factor / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL24 / 50S ribosomal protein L23
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D
AuthorsMerz, F. / Boehringer, D. / Schaffitzel, C. / Preissler, S. / Hoffmann, A. / Maier, T. / Rutkowska, A. / Lozza, J. / Ban, N. / Bukau, B. / Deuerling, E.
CitationJournal: EMBO J / Year: 2008
Title: Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
Authors: Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling /
Abstract: Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions ...Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.
History
DepositionApr 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Derived calculations / Other / Version format compliance
Revision 1.2Aug 7, 2013Group: Other / Refinement description
Revision 1.3Aug 23, 2017Group: Data collection / Refinement description
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_imaging / em_software
Item: _em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max ..._em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1499
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1499
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIGGER FACTOR
B: 50S RIBOSOMAL PROTEIN L23
C: 50S RIBOSOMAL PROTEIN L24
D: 50S RIBOSOMAL PROTEIN L29


Theoretical massNumber of molelcules
Total (without water)78,4884
Polymers78,4884
Non-polymers00
Water0
1


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

-
Components

#1: Protein TRIGGER FACTOR / Coordinate model: Cα atoms only


Mass: 48771.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BASED ON PDB 1W26_A. RESIDUES 22-62 WERE REPLACED WITH THE CORRESPONDING RESIDUES OF PDB 1OMS_B
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: BASED ON PDB 1W26_A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A850
#2: Protein 50S RIBOSOMAL PROTEIN L23 / / Coordinate model: Cα atoms only


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_T / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: Q0TCE3, UniProt: P0ADZ0*PLUS
#3: Protein 50S RIBOSOMAL PROTEIN L24 / / Coordinate model: Cα atoms only


Mass: 11208.054 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-104 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_U / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P60624
#4: Protein 50S RIBOSOMAL PROTEIN L29 / / Coordinate model: Cα atoms only


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BASED ON PDB 2AW4_X / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7M6

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME
Type: RIBOSOME
Buffer solutionName: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL
pH: 7.5
Details: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 0.5 MG/ML CHLORAMPHENICOL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderTemperature: 88 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1MOLREPmolecular replacement
2IMAGIC53D reconstruction
3SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 19 Å / Nominal pixel size: 4.233 Å / Actual pixel size: 4.233 Å / Details: FITTING OF CRYSTAL STRUCTURES INTO MAP EMD-1499 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-ID
12AW4

2aw4
PDB Unreleased entry

1
21W26

1w26

1
RefinementHighest resolution: 19 Å
Refinement stepCycle: LAST / Highest resolution: 19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms695 0 0 0 695

+
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