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- PDB-8rxc: RadA helicase from Streptococcus pneumoniae coordinating dsDNA -

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Basic information

Entry
Database: PDB / ID: 8rxc
TitleRadA helicase from Streptococcus pneumoniae coordinating dsDNA
Components
  • DNA repair protein RadA
  • Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)
  • Poly-dT 30 bp
KeywordsDNA BINDING PROTEIN / Helicase Translocase natural transformation
Function / homology
Function and homology information


recombinational repair / ATP-dependent DNA damage sensor activity / damaged DNA binding / hydrolase activity / zinc ion binding / ATP binding / cytosol
Similarity search - Function
DNA repair protein RadA / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / Subunit ChlI of Mg-chelatase / AAA domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities ...DNA repair protein RadA / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / Subunit ChlI of Mg-chelatase / AAA domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA (> 100) / DNA repair protein RadA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsTalachia Rosa, L. / Fronzes, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO J / Year: 2024
Title: Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria.
Authors: Leonardo Talachia Rosa / Émeline Vernhes / Anne-Lise Soulet / Patrice Polard / Rémi Fronzes /
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 ...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.
History
DepositionFeb 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Oct 30, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Oct 30, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 30, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA repair protein RadA
C: DNA repair protein RadA
B: DNA repair protein RadA
A: DNA repair protein RadA
F: DNA repair protein RadA
E: DNA repair protein RadA
G: Poly-dT 30 bp
H: Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,07918
Polymers354,3418
Non-polymers2,73810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DNA repair protein RadA


Mass: 51526.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: radA, A5N45_07085, GM529_10050, GM532_03345, GM536_10290, GM537_09620, GM538_09765, GM539_03745, GM543_09545, GM544_10415, GM546_02225
Production host: Escherichia coli (E. coli) / References: UniProt: A0A237IXT5
#2: DNA chain Poly-dT 30 bp


Mass: 9080.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)


Mass: 36098.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RadA helicase from Streptococcus pneumoniae coordinating dsDNA
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.35 mg/ml protein and 100 uM of hybrid DNA
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54.04 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303651 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419540
ELECTRON MICROSCOPYf_angle_d0.71126636
ELECTRON MICROSCOPYf_dihedral_angle_d17.0662967
ELECTRON MICROSCOPYf_chiral_restr0.0463185
ELECTRON MICROSCOPYf_plane_restr0.0053264

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