[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleLarge-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.
Journal, issue, pagesCell, Vol. 167, Issue 1, Page 133-144.e13, Year 2016
Publish dateSep 22, 2016
AuthorsTanweer Hussain / Jose L Llácer / Brian T Wimberly / Jeffrey S Kieft / V Ramakrishnan /
PubMed AbstractIn bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 ...In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.
External linksCell / PubMed:27662086 / PubMed Central
MethodsEM (single particle)
Resolution3.55 - 9.7 Å
Structure data

4073

5lmn

EMDB-4073, PDB-5lmn:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A)
Method: EM (single particle) / Resolution: 3.55 Å

4074

5lmo

EMDB-4074, PDB-5lmo:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1B)
Method: EM (single particle) / Resolution: 4.3 Å

4075

5lmp

EMDB-4075, PDB-5lmp:
Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C)
Method: EM (single particle) / Resolution: 5.35 Å

4076

5lmq

EMDB-4076, PDB-5lmq:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form (state-2A)
Method: EM (single particle) / Resolution: 4.2 Å

4077

5lmr

EMDB-4077, PDB-5lmr:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)
Method: EM (single particle) / Resolution: 4.45 Å

4078

5lms

EMDB-4078, PDB-5lms:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2C)
Method: EM (single particle) / Resolution: 5.1 Å

4079

5lmt

EMDB-4079, PDB-5lmt:
Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-3)
Method: EM (single particle) / Resolution: 4.15 Å

4080

5lmu

EMDB-4080: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, closed form (state-4)
PDB-5lmu: Structure of bacterial 30S-IF3-mRNA-tRNA translation pre-initiation complex, closed form (state-4)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-4081:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA translation pre-initiation complex (state-I)
Method: EM (single particle) / Resolution: 9.7 Å

EMDB-4082:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation complex(state-II)
Method: EM (single particle) / Resolution: 8.3 Å

4083

5lmv

EMDB-4083, PDB-5lmv:
Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation complex(state-III)
Method: EM (single particle) / Resolution: 4.9 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-A:
ADENOSINE-5'-MONOPHOSPHATE

ChemComp-G:
GUANOSINE-5'-MONOPHOSPHATE

ChemComp-U:
URIDINE-5'-MONOPHOSPHATE

ChemComp-FME:
N-FORMYLMETHIONINE

Source
  • thermus thermophilus hb8 (bacteria)
  • thermus thermophilus (bacteria)
  • thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (bacteria)
  • escherichia coli (E. coli)
KeywordsRIBOSOME / translation / initiation factors / 30S / IF1 / IF3 / PIC / Thermus thermophilus / tRNAi / IF2

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more