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- PDB-9d4n: The cryo-EM structure of the yeast Dmc1 filament bound to ssDNA i... -

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Basic information

Entry
Database: PDB / ID: 9d4n
TitleThe cryo-EM structure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Meiotic recombination protein DMC1
KeywordsDNA BINDING PROTEIN/DNA / DNA Repair / Homologous Recombination / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


meiotic joint molecule formation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity ...meiotic joint molecule formation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / synaptonemal complex assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / ATPase inhibitor activity / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / sporulation resulting in formation of a cellular spore / 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'-TRIPHOSPHATE / DNA / DNA (> 10) / Meiotic recombination protein DMC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShin, Y. / Greene, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-MCB1817315 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP
Authors: Shin, Y. / Greene, E.C.
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 19, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Data processing / Derived calculations / Structure summary
Category: atom_site / em_3d_reconstruction ...atom_site / em_3d_reconstruction / em_admin / em_imaging / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn
Item: _em_3d_reconstruction.num_particles / _em_admin.last_update ..._em_3d_reconstruction.num_particles / _em_admin.last_update / _em_imaging.microscope_model / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list
Description: Atomic clashes / Details: Metal atom clash corrected. / Provider: author / Type: Coordinate replacement

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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
X: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,71025
Polymers225,3767
Non-polymers3,33518
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: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / 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: helical reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of yeast Dmc1 filament bound on ssDNA in the presence of ATP
Type: COMPLEX / Entity ID: #1-#2 / 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
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 56 ° / Axial rise/subunit: 16 Å / Axial symmetry: C1
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364408 / Symmetry type: HELICAL

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