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- PDB-9e6l: Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to ... -

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Basic information

Entry
Database: PDB / ID: 9e6l
TitleCryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA repair and recombination protein RAD54
  • DNA repair protein RAD51
KeywordsRECOMBINATION/DNA / Rad51 / DNA recombinase / Homologous recombination / DNA repair / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / mitochondrial chromosome / mitotic recombination-dependent replication fork processing ...double-strand break repair via synthesis-dependent strand annealing / Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / DNA geometric change / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA translocase activity / DNA strand exchange activity / DNA clamp loader activity / telomere maintenance via recombination / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / mitochondrial DNA repair / nuclear chromosome / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / G2/M transition of mitotic cell cycle / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / mitochondrial matrix / chromatin remodeling / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Rad54, N-terminal / Rad54 N terminal / : / DNA recombination/repair protein Rad51 / 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 ...Rad54, N-terminal / Rad54 N terminal / : / DNA recombination/repair protein Rad51 / 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 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding 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) / DNA repair protein RAD51 / DNA repair and recombination protein RAD54
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShin, Y. / Greene, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of yeast Rad51 nucleoprotein filament bound to Rad54peptide
Authors: Shin, Y. / Greene, E.C.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 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
G: DNA repair and recombination protein RAD54
H: DNA repair and recombination protein RAD54
I: DNA repair and recombination protein RAD54
J: DNA repair and recombination protein RAD54
K: DNA repair and recombination protein RAD54
X: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
C: DNA repair protein RAD51
F: DNA repair protein RAD51
B: DNA repair protein RAD51
E: DNA repair protein RAD51
A: DNA repair protein RAD51
D: DNA repair protein RAD51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,51430
Polymers235,18012
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/peptide
DNA repair and recombination protein RAD54


Mass: 4033.730 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32863, DNA helicase
#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: Protein
DNA repair protein RAD51


Mass: 34930.070 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD51, YER095W / Production host: Escherichia coli (E. coli) / References: UniProt: P25454
#4: 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
#5: 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: single particle reconstruction

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Sample preparation

ComponentName: Rad51 nucleoprotein filament bound to Rad54 peptide / Type: COMPLEX / Entity ID: #1-#3 / 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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 59.51 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 363379 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216841
ELECTRON MICROSCOPYf_angle_d0.42722822
ELECTRON MICROSCOPYf_dihedral_angle_d10.272472
ELECTRON MICROSCOPYf_chiral_restr0.0392597
ELECTRON MICROSCOPYf_plane_restr0.0022898

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