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- EMDB-72162: Rad55-Rad57-SHU bound to ssDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-72162
TitleRad55-Rad57-SHU bound to ssDNA
Map dataRad55-Rad57-SHU bound to ssDNA
Sample
  • Complex: Rad55-Rad57-SHU bound to ssDNA
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
    • Protein or peptide: DNA repair protein RAD57
    • Protein or peptide: Chromosome segregation in meiosis protein 2
    • Protein or peptide: Platinum sensitivity protein 3
    • Protein or peptide: Suppressor of HU sensitivity involved in recombination protein 1
    • Protein or peptide: Suppressor of hydroxyurea sensitivity protein 2
    • DNA: ssDNA (6-mer)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsHomologous 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 / 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 ...Shu complex / positive regulation of single-strand break repair via homologous recombination / 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 / 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 / DNA replication origin binding / ATP-dependent activity, acting on DNA / replication fork / double-strand break repair / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / methylation / DNA recombination / DNA repair / nucleolus / DNA binding / ATP binding / metal ion 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 and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / 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
Suppressor of hydroxyurea sensitivity protein 2 / Methylated-DNA--protein-cysteine methyltransferase / DNA repair protein RAD57 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYatskevich S / Koo CW / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Rad51 Paralog Complex Dynamically Templates Rad51 Filament Nucleation
Authors: Yatskevich S / Koo CW / Ciferri C
History
DepositionAug 15, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72162.png

Downloads & links

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Map

FileDownload / File: emd_72162.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRad55-Rad57-SHU bound to ssDNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 400 pix.
= 362.5 Å		0.91 Å/pix.
x 400 pix.
= 362.5 Å		0.91 Å/pix.
x 400 pix.
= 362.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.90625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.26894665 - 0.51613677
Average (Standard dev.)-0.00040077613 (±0.009743182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 362.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72162_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map A

Fileemd_72162_additional_1.map
AnnotationAdditional Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Additional Map 2

Fileemd_72162_additional_2.map
AnnotationAdditional Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map 3

Fileemd_72162_additional_3.map
AnnotationAdditional Map 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72162_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72162_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rad55-Rad57-SHU bound to ssDNA

EntireName: Rad55-Rad57-SHU bound to ssDNA
Components
  • Complex: Rad55-Rad57-SHU bound to ssDNA
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
    • Protein or peptide: DNA repair protein RAD57
    • Protein or peptide: Chromosome segregation in meiosis protein 2
    • Protein or peptide: Platinum sensitivity protein 3
    • Protein or peptide: Suppressor of HU sensitivity involved in recombination protein 1
    • Protein or peptide: Suppressor of hydroxyurea sensitivity protein 2
    • DNA: ssDNA (6-mer)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Rad55-Rad57-SHU bound to ssDNA

SupramoleculeName: Rad55-Rad57-SHU bound to ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 226.81 KDa

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Macromolecule #1: Methylated-DNA--protein-cysteine methyltransferase,DNA repair pro...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 70.243594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSMDKDCEM KRTTLDSPLG KLELSGCEQG LHRIIFLGKG TSAADAVEVP APAAVLGGP EPLMQATAWL NAYFHQPEAI EEFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYSH LAALAGNPAA T AAVKTALS ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSMDKDCEM KRTTLDSPLG KLELSGCEQG LHRIIFLGKG TSAADAVEVP APAAVLGGP EPLMQATAWL NAYFHQPEAI EEFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYSH LAALAGNPAA T AAVKTALS GNPVPILIPC HRVVQGDLDV GGYEGGLAVK EWLLAHEGHR LGKPGLGGSE NLYFQGSMSL GIPLSQLIVE SP KPLSSGI TGLDEILNLG FQARSIYEIF GPPGIGKTNF GIQLVCNSLE GIQQSEINDD KILWIETFQE MPINILRERF QKF KIVEEN VKRVRITKFG QLLYFFQNLF KLSQSVRYKL VIIDGFSQLV CDHLCTLSKR GGGMIDKTIH ELKCRHLILI FTVM TKYTH STGSTIIVLN DCMNTAFQSN EFESLEEYYE ILDDGSNFFV NSNNERRKNN VHILKSALVA NIAMGSKDST WEVFL RDRI GLFRDWNEQV DETVFVKSKR VKASSSQSNE GCTTIKEMRI NKRNFENLRI AIVFNLHGED RKREGRNLKR SRSSDD RNY IVKFDFDKAT GQLRDIIDLK PDTANIASFP TLSTSSSSCS QVFNNIDSND NPLPNAEGKE EIIYDSEG

UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, DNA repair protein RAD55

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Macromolecule #2: DNA repair protein RAD57

MacromoleculeName: DNA repair protein RAD57 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.308301 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPRALSIKFD NTYMDLYDEL PESKLLYDEE FSYLLDAVRQ NGVCVVDFLT LTPKELARLI QRSINEVFRF QQLLVHEYNE KYLEICEKN SISPDNGPEC FTTADVAMDE LLGGGIFTHG ITEIFGESST GKSQLLMQLA LSVQLSEPAG GLGGKCVYIT T EGDLPTQR ...String:
MPRALSIKFD NTYMDLYDEL PESKLLYDEE FSYLLDAVRQ NGVCVVDFLT LTPKELARLI QRSINEVFRF QQLLVHEYNE KYLEICEKN SISPDNGPEC FTTADVAMDE LLGGGIFTHG ITEIFGESST GKSQLLMQLA LSVQLSEPAG GLGGKCVYIT T EGDLPTQR LESMLSSRPA YEKLGITQSN IFTVSCNDLI NQEHIINVQL PILLERSKGS IKLVIIDSIS HHLRVELQNK SF RESQENK NYLDRMAEKL QILAHDYSLS VVVANQVGDK PLANSPVAHR TYVTDYDYQL GWLVGWKNST ILYRQMNSLL GAS SNNDEI LSDDEDYMLI ERVMSTVNDR NYDFFSKKKP PIIENKTVER NSSSPISRQS KKRKFDYRVP NLGLTWSNHV STRI LLQKS FKASTIIQRG EAHLYKGGDS ASFWQVKRTM KVVYSTFAKP GQIAYQITKR GIETA

UniProtKB: DNA repair protein RAD57

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Macromolecule #3: Chromosome segregation in meiosis protein 2

MacromoleculeName: Chromosome segregation in meiosis protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.98368 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEYEDLELIT IWPSPTKNKL CQFIKQNLSK EHVVTQLFFI DATSSFPLSQ FQKLVPPTLP ENVRIYENIR INTCLDLEEL SAITVKLLQ ILSMNKINAQ RGTEDAVTEP LKIILYINGL EVMFRNSQFK SSPQRSHELL RDTLLKLRVM GNDENENASI R TLLEFPKE ...String:
MEYEDLELIT IWPSPTKNKL CQFIKQNLSK EHVVTQLFFI DATSSFPLSQ FQKLVPPTLP ENVRIYENIR INTCLDLEEL SAITVKLLQ ILSMNKINAQ RGTEDAVTEP LKIILYINGL EVMFRNSQFK SSPQRSHELL RDTLLKLRVM GNDENENASI R TLLEFPKE QLLDYYLKKN NNTRTSSVRS KRRRIKNGDS LAEYIWKYYA DSLFE

UniProtKB: Chromosome segregation in meiosis protein 2

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Macromolecule #4: Platinum sensitivity protein 3

MacromoleculeName: Platinum sensitivity protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.385123 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQM EVLKNIRIYP LSNFITSTKN YINLPNELRN LISEEQESKL GFLHIIESD FKPSVALQKL VNCTTGDEKI LIIDIVSIWS QQKQRQHGAI YMNSLSCINI TGLIVFLELL YDSPMDALRR C QVDNFNFQ ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQM EVLKNIRIYP LSNFITSTKN YINLPNELRN LISEEQESKL GFLHIIESD FKPSVALQKL VNCTTGDEKI LIIDIVSIWS QQKQRQHGAI YMNSLSCINI TGLIVFLELL YDSPMDALRR C QVDNFNFQ LRGIVIDNLS FLNFESDKNY DVINLSKFEK LFKILRKLRE FLGCWIITKS FPTDFYNGIE NTLVDKWSIK RK SGVTLYP TKLPDSYMKG MDLIIYREVV DGRPQYRRIA ALEE

UniProtKB: Platinum sensitivity protein 3

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

MacromoleculeName: Suppressor of HU sensitivity involved in recombination protein 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.138637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MQFEERLQQL VESDWSLDQS SPNVLVIVLG DTARKYVELG GLKEHVTTNT VAGHVASRER VSVVFLGRVK YLYMYLTRMQ AQANGPQYS NVLVYGLWDL TATQDGPQQL RLLSLVLRQC LSLPSKVEFY PEPPSSSVPA RLLRFWDHII R

UniProtKB: Suppressor of HU sensitivity involved in recombination protein 1

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Macromolecule #6: Suppressor of hydroxyurea sensitivity protein 2

MacromoleculeName: Suppressor of hydroxyurea sensitivity protein 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.179885 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQG SKDVIEYSKL FAKLVNTNDD TKLDDTIASF LYYMFPRELF IRAISLLES SDMFIYILDR VHNKEGNEHT SLIDVLVDEF YKGSSNSLLE YRLIVKDTND GAPPILVDIA HWFCSCEEFC K YFHEALEK ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KSGENLYFQG SKDVIEYSKL FAKLVNTNDD TKLDDTIASF LYYMFPRELF IRAISLLES SDMFIYILDR VHNKEGNEHT SLIDVLVDEF YKGSSNSLLE YRLIVKDTND GAPPILVDIA HWFCSCEEFC K YFHEALEK TDEKEELHDV LINEVDDHLQ FSDDRFAQLD PHSLSKQWYF KFDKVCCSHL LAFSILLRSS INVLKFFTVN SN KVFVIAI DNIDEWLNLH INIVE

UniProtKB: Suppressor of hydroxyurea sensitivity protein 2

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Macromolecule #7: ssDNA (6-mer)

MacromoleculeName: ssDNA (6-mer) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.780199 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17317
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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