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- PDB-9q2f: Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 9q2f
TitleRad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP
Components
  • (DNA repair protein ...) x 2
  • (Suppressor of ...) x 2
  • Chromosome segregation in meiosis protein 2
  • Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
  • Platinum sensitivity protein 3
  • ssDNA (9-mer)
KeywordsDNA BINDING PROTEIN/DNA / Homologous Recombination Complex / Rad51 Paralog Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Shu complex / positive regulation of single-strand break repair via homologous recombination / Presynaptic phase of homologous DNA pairing and strand exchange / meiotic joint molecule formation / error-free postreplication DNA repair / heteroduplex formation / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / methylated-DNA-[protein]-cysteine S-methyltransferase ...Shu complex / positive regulation of single-strand break repair via homologous recombination / Presynaptic phase of homologous DNA pairing and strand exchange / meiotic joint molecule formation / error-free postreplication DNA repair / heteroduplex formation / Rad51C-XRCC3 complex / Rad51B-Rad51C-Rad51D-XRCC2 complex / meiotic DNA recombinase assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / meiotic chromosome segregation / maintenance of rDNA / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / mitochondrial DNA repair / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / telomere maintenance via recombination / reciprocal meiotic recombination / recombinational repair / error-free translesion synthesis / ATP-dependent DNA damage sensor activity / nuclear chromosome / DNA replication origin binding / ATP-dependent activity, acting on DNA / replication fork / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / nucleotide-excision repair / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / methylation / DNA recombination / mitochondrial matrix / DNA repair / nucleolus / DNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / : / : / Methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC ...Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / : / : / Methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / KaiC / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding 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 / : / SAM-like Helix-hairpin-helix tandem / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / Suppressor of hydroxyurea sensitivity protein 2 / Methylated-DNA--protein-cysteine methyltransferase / DNA repair protein RAD57 / DNA repair protein RAD51 / Suppressor of HU sensitivity involved in recombination protein 1 / DNA repair protein RAD55 / Chromosome segregation in meiosis protein 2 / Platinum sensitivity protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsYatskevich, S. / Koo, C.W. / Ciferri, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Rad51 Paralog Complex Dynamically Templates Rad51 Filament Nucleation
Authors: Yatskevich, S. / Koo, C.W. / Ciferri, C.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
B: DNA repair protein RAD57
C: Chromosome segregation in meiosis protein 2
D: Platinum sensitivity protein 3
E: Suppressor of HU sensitivity involved in recombination protein 1
F: Suppressor of hydroxyurea sensitivity protein 2
G: DNA repair protein RAD51
H: ssDNA (9-mer)
I: DNA repair protein RAD51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,45914
Polymers320,4119
Non-polymers1,0475
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

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Protein , 3 types, 3 molecules ACD

#1: Protein Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55 / 6-O-methylguanine-DNA methyltransferase / O-6-methylguanine-DNA-alkyltransferase


Mass: 70243.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD55, YDR076W, D4426 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: E5BBQ0, UniProt: P38953, methylated-DNA-[protein]-cysteine S-methyltransferase
#3: Protein Chromosome segregation in meiosis protein 2


Mass: 24983.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSM2, YIL132C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40465
#4: Protein Platinum sensitivity protein 3


Mass: 32385.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PSY3, YLR376C, L8039.17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12318

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DNA repair protein ... , 2 types, 3 molecules BGI

#2: Protein DNA repair protein RAD57


Mass: 52308.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD57, YDR004W, YD8119.10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25301
#7: Protein DNA repair protein RAD51


Mass: 45239.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD51, YER095W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25454

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Suppressor of ... , 2 types, 2 molecules EF

#5: Protein Suppressor of HU sensitivity involved in recombination protein 1


Mass: 17138.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SHU1, YHL006C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38751
#6: Protein Suppressor of hydroxyurea sensitivity protein 2


Mass: 30179.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SHU2, C1Q_04575 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7GVQ9

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DNA chain , 1 types, 1 molecules H

#8: DNA chain ssDNA (9-mer)


Mass: 2692.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 5 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Molecular weightValue: 0.271980 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.2
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11289 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 132.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006616775
ELECTRON MICROSCOPYf_angle_d0.841122718
ELECTRON MICROSCOPYf_chiral_restr0.05472612
ELECTRON MICROSCOPYf_plane_restr0.0082857
ELECTRON MICROSCOPYf_dihedral_angle_d14.96946254

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