8RXC | pdb_00008rxc

RadA helicase from Streptococcus pneumoniae coordinating dsDNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria.

Rosa, L.T.Vernhes, E.Soulet, A.L.Polard, P.Fronzes, R.

(2024) EMBO J 43: 6180-6198

  • DOI: https://doi.org/10.1038/s44318-024-00264-5
  • Primary Citation of Related Structures:  
    8RXC, 8RXD, 8RXK, 8RXS, 8RXT

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Structure and Function of Bacterial Nanomachines-Institut Européen de Chimie et Biologie, Microbiologie fondamentale et pathogénicité, UMR 5234, CNRS, University of Bordeaux, 2 rue Robert Escarpit, 33600, Pessac, France.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RadA473Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A237IXT5 (Streptococcus pneumoniae)
Explore A0A237IXT5 
Go to UniProtKB:  A0A237IXT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A237IXT5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
Poly-dT 30 bp30synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)120synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
I [auth D],
K [auth C],
N [auth B],
O [auth F],
Q [auth E]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth D],
L [auth C],
M [auth B],
P [auth F],
R [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection