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- PDB-9njr: The Cryo-EM structure of the yeast Dmc1-ssDNA nucleoprotein filam... -

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Basic information

Entry
Database: PDB / ID: 9njr
TitleThe Cryo-EM structure of the yeast Dmc1-ssDNA nucleoprotein filament ADP bound state
ComponentsMeiotic recombination protein DMC1
KeywordsDNA BINDING PROTEIN / DNA Repair / Homologous Recombination
Function / homology
Function and homology information


meiotic joint molecule formation / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / sporulation resulting in formation of a cellular spore ...meiotic joint molecule formation / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / sporulation resulting in formation of a cellular spore / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / meiotic cell cycle / single-stranded DNA binding / double-stranded DNA binding / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Meiotic recombination protein DMC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsShin, Y. / Greene, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-MCB1817315 United States
CitationJournal: J Biol Chem / Year: 2025
Title: ATP hydrolysis-driven structural transitions within the Saccharomyces cerevisiae Rad51 and Dmc1 nucleoprotein filaments.
Authors: Yeonoh Shin / Stefan Y Kim / Eric C Greene /
Abstract: Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family ...Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family of DNA recombinases and is responsible for guiding the DNA pairing reactions that take place in HR during mitosis. Dmc1 is a meiosis-specific paralog of Rad51 and is responsible for the DNA pairing reactions that take place in HR during meiosis. Rad51 and Dmc1 are both ATP-dependent DNA-binding proteins and both form extended helical filaments on ssDNA, which are key intermediates in HR. The stability of these nucleoprotein filaments is highly regulated and is also tightly coupled to nucleotide binding and hydrolysis. ATP binding promotes filament assembly, whereas the hydrolysis of ATP to ADP reduces filament stability to promote filament disassembly. Here, we present cryo-EM structures of the Saccharomyces cerevisiae recombinases Rad51 and Dmc1 in the ADP-bound states and provide a detailed structural comparison to the ATP-bound filaments. Our findings yield insights into the structural transitions that take place during the hydrolysis of ATP to ADP and suggest a new model for how these structural changes may be linked to nucleoprotein filament disassembly.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meiotic recombination protein DMC1
B: Meiotic recombination protein DMC1
C: Meiotic recombination protein DMC1
D: Meiotic recombination protein DMC1
E: Meiotic recombination protein DMC1
F: Meiotic recombination protein DMC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,30012
Polymers219,9456
Non-polymers1,3556
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
Meiotic recombination protein DMC1


Mass: 36657.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DMC1, ISC2, YER179W / Production host: Escherichia coli (E. coli) / References: UniProt: P25453
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cryo-EM structure of yeast Dmc1 - ssDNA nucleoprotein filament ADP bound state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1750 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 960233 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314042
ELECTRON MICROSCOPYf_angle_d0.61118893
ELECTRON MICROSCOPYf_dihedral_angle_d5.7761961
ELECTRON MICROSCOPYf_chiral_restr0.0452175
ELECTRON MICROSCOPYf_plane_restr0.0042436

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