[English] 日本語
Yorodumi
- PDB-3j4j: Model of full-length T. thermophilus Translation Initiation Facto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j4j
TitleModel of full-length T. thermophilus Translation Initiation Factor 2 refined against its cryo-EM density from a 30S Initiation Complex map
ComponentsTranslation initiation factor IF-2
KeywordsTRANSLATION / IF2 / GTP-Binding Protein / fMet-tRNA binding / ribosome binding
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation elongation factor EFTu-like, domain 2 ...Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Translation initiation factor IF-2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsSimonetti, A. / Marzi, S. / Billas, I.M.L. / Tsai, A. / Fabbretti, A. / Myasnikov, A. / Roblin, P. / Vaiana, A.C. / Hazemann, I. / Eiler, D. ...Simonetti, A. / Marzi, S. / Billas, I.M.L. / Tsai, A. / Fabbretti, A. / Myasnikov, A. / Roblin, P. / Vaiana, A.C. / Hazemann, I. / Eiler, D. / Steitz, T.A. / Puglisi, J.D. / Gualerzi, C.O. / Klaholz, B.P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor.
Authors: Angelita Simonetti / Stefano Marzi / Isabelle M L Billas / Albert Tsai / Attilio Fabbretti / Alexander G Myasnikov / Pierre Roblin / Andrea C Vaiana / Isabelle Hazemann / Daniel Eiler / ...Authors: Angelita Simonetti / Stefano Marzi / Isabelle M L Billas / Albert Tsai / Attilio Fabbretti / Alexander G Myasnikov / Pierre Roblin / Andrea C Vaiana / Isabelle Hazemann / Daniel Eiler / Thomas A Steitz / Joseph D Puglisi / Claudio O Gualerzi / Bruno P Klaholz /
Abstract: Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle ...Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNA(fMet) positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.
History
DepositionAug 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2448
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2448
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2448
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Translation initiation factor IF-2


Theoretical massNumber of molelcules
Total (without water)62,4941
Polymers62,4941
Non-polymers00
Water0
1


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

-
Components

#1: Protein Translation initiation factor IF-2


Mass: 62494.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infB, TTHA0699 / Production host: Escherichia coli (E. coli) / References: UniProt: P48515

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-ID
1T. thermophilus 30S initiation complex with 30S, fMet-tRNA, IF2-GTP, IF1, and mRNARIBOSOME0
2Initiation Factor 21
Buffer solutionName: 10 mM HEPES, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 8 mM magnesium acetate, 1 mM DTT
pH: 7.5
Details: 10 mM HEPES, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 8 mM magnesium acetate, 1 mM DTT
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: Vitrification carried out in liquid ethane

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Oct 9, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 150 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: -3500 nm / Nominal defocus min: -1500 nm
Specimen holderTemperature: 70 K
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1DireXmodel fitting
2EMAN23D reconstruction
3IMAGIC3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 11.5 Å / Num. of particles: 13000 / Nominal pixel size: 1.92 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: METHOD--cross-correlation gradient based REFINEMENT PROTOCOL--flexible fitting, dynamic elastic network
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 0 4383

+
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