[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

TitleStructural insights into the mechanism of DNA branch migration during homologous recombination in bacteria.
Journal, issue, pagesEMBO J, Vol. 43, Issue 23, Page 6180-6198, Year 2024
Publish dateOct 18, 2024
AuthorsLeonardo Talachia Rosa / Émeline Vernhes / Anne-Lise Soulet / Patrice Polard / Rémi Fronzes /
PubMed AbstractSome DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly ...Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly conserved bacterial helicase involved in DNA repair throughout all bacterial species. In Gram-positive Firmicutes, it also has a role in natural transformation, while in Gram-negative bacteria, ComM is the canonical transformation-specific helicase. Both RadA and ComM helicases form hexameric rings and use ATP hydrolysis as an energy source to propel themselves along DNA. In this study, we present the cryoEM structures of RadA and ComM interacting with DNA and ATP analogs. These structures reveal important molecular interactions that couple ATP hydrolysis and DNA binding in RadA, as well as the role of the Lon protease-like domain, shared by RadA and ComM, in this process. Taken together, these results provide new molecular insights into the mechanisms of DNA branch migration in different pathways of homologous recombination.
External linksEMBO J / PubMed:39424952 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.01 Å
Structure data

19573

8rxc

EMDB-19573, PDB-8rxc:
RadA helicase from Streptococcus pneumoniae coordinating dsDNA
Method: EM (single particle) / Resolution: 3.15 Å

19574

8rxd

EMDB-19574, PDB-8rxd:
ComM helicase from Legionella pneumophila, coordinating dsDNA and AMP-PNP
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-19575: ComM helicase hexamer from Legionella pneumophila bound to dsDNA - Alternative conformation map
Method: EM (single particle) / Resolution: 3.37 Å

19577

8rxk

EMDB-19577, PDB-8rxk:
ComM helicase from Legionella pneumophila, coordinating dsDNA and AMP-PNP
Method: EM (single particle) / Resolution: 3.23 Å

19578

8rxs

EMDB-19578, PDB-8rxs:
ComM helicase from Legionella pneumophila - Lon domain hexamer
Method: EM (single particle) / Resolution: 2.8 Å

19579

8rxt

EMDB-19579, PDB-8rxt:
ComM helicase hexamer in abscence o DNA
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-19580: ComM helicase dodecamers from Legionella maltophila
Method: EM (single particle) / Resolution: 4.01 Å

EMDB-19581: ComM helicase hexamer from Legionella maltophila coordinating dsDNA- Consensus map
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

Source
  • streptococcus pneumoniae (bacteria)
  • synthetic construct (others)
  • legionella pneumophila (bacteria)
KeywordsDNA BINDING PROTEIN / Helicase Translocase natural transformation / Helicase / Translocase / natural transformation

+
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