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- PDB-8rxt: ComM helicase hexamer in abscence o DNA -

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Basic information

Entry
Database: PDB / ID: 8rxt
TitleComM helicase hexamer in abscence o DNA
ComponentsCompetence related protein ComM
KeywordsDNA BINDING PROTEIN / Helicase / Translocase / natural transformation
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
Mg chelatase-related protein / Mg chelatase-related protein, C-terminal domain / Magnesium chelatase, subunit ChlI C-terminal / Subunit ChlI of Mg-chelatase / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities ...Mg chelatase-related protein / Mg chelatase-related protein, C-terminal domain / Magnesium chelatase, subunit ChlI C-terminal / Subunit ChlI of Mg-chelatase / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Competence related protein ComM
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 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 7, 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
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Revision 1.0Oct 30, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.1Dec 11, 2024Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 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
A: Competence related protein ComM
B: Competence related protein ComM
C: Competence related protein ComM
D: Competence related protein ComM
E: Competence related protein ComM
F: Competence related protein ComM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,12110
Polymers335,0966
Non-polymers2,0254
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
Competence related protein ComM


Mass: 55849.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: comM, lpg0590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZXZ0
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: ComM / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Legionella pneumophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 54.61 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78222 / Symmetry type: POINT

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