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- PDB-9ui9: structure of a 12 base pair Rad51 D-loop complex -

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Basic information

Entry
Database: PDB / ID: 9ui9
Titlestructure of a 12 base pair Rad51 D-loop complex
Components
  • (DNA (48-MER)) x 2
  • DNA (35-MER)
  • DNA repair protein RAD51 homolog 1
KeywordsDNA BINDING PROTEIN/DNA / homologous recombination / strand exchange / D-loop / RECOMBINATION / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly ...Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / cellular response to hydroxyurea / synaptonemal complex / DNA strand exchange activity / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / telomere maintenance via recombination / single-stranded DNA helicase activity / reciprocal meiotic recombination / regulation of double-strand break repair via homologous recombination / ATP-dependent DNA damage sensor activity / nuclear chromosome / cellular response to alkaloid / replication fork processing / response to X-ray / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / telomere organization / condensed nuclear chromosome / cellular response to ionizing radiation / meiotic cell cycle / male germ cell nucleus / cellular response to gamma radiation / double-strand break repair via homologous recombination / PML body / response to toxic substance / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / DNA damage response / centrosome / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 / DNA / DNA (> 10) / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLuo, S.C. / Ho, M.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-TP-113-L01 to M.C.H Taiwan
CitationJournal: To Be Published
Title: Mechanism of strand exchange of eukaryotic homologous recombination from RAD51 D-loop structures
Authors: Luo, S.C.
History
DepositionApr 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA repair protein RAD51 homolog 1
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
U: DNA (48-MER)
T: DNA (48-MER)
H: DNA repair protein RAD51 homolog 1
I: DNA repair protein RAD51 homolog 1
L: DNA (35-MER)
A: DNA repair protein RAD51 homolog 1
B: DNA repair protein RAD51 homolog 1
C: DNA repair protein RAD51 homolog 1
D: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,95230
Polymers396,17712
Non-polymers4,77518
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 9 molecules EFGHIABCD

#1: Protein
DNA repair protein RAD51 homolog 1 / RAD51 homolog A


Mass: 39557.750 Da / Num. of mol.: 9 / Mutation: S208E/A209D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rad51, Rad51a, Reca / Production host: Escherichia coli (E. coli) / References: UniProt: Q08297

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DNA chain , 3 types, 3 molecules UTL

#2: DNA chain DNA (48-MER)


Mass: 14720.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3'-tilt dsDNA / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (48-MER)


Mass: 14856.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-tilt dsDNA / Source: (synth.) Mus musculus (house mouse)
#4: DNA chain DNA (35-MER)


Mass: 10580.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ssDNA, the 3'-end contains extra eight nucleotides (T) that is built based on density map due to end to end fusion of Rad51.
Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 2 types, 18 molecules

#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg

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Details

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: mRAD51 D-loop / Type: COMPLEX / Details: mRAD51 protein filament in complex with dsDNA / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: RecA-deficient BLR strain
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45865 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424133
ELECTRON MICROSCOPYf_angle_d0.75432990
ELECTRON MICROSCOPYf_dihedral_angle_d20.4074409
ELECTRON MICROSCOPYf_chiral_restr0.0443749
ELECTRON MICROSCOPYf_plane_restr0.0053937

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