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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP | |||||||||
Map data | consensus | |||||||||
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Keywords | Homologous Recombination Complex / Rad51 Paralog Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
| Function / homology | Function and homology informationShu 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 / maintenance of rDNA / meiotic chromosome segregation / 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 / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / replication fork / double-strand break repair via homologous recombination / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / single-stranded DNA binding / site of double-strand break / DNA recombination / double-stranded DNA binding / mitochondrial matrix / DNA repair / nucleolus / DNA binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Yatskevich S / Koo CW / Ciferri C | |||||||||
| Funding support | 1 items
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Citation | Journal: Mol Cell / Year: 2026Title: Yeast Rad55-Rad57-SHU paralog complex dynamically promotes Rad51 filament formation. Authors: Christopher W Koo / Steven K Gore / Soo Y Ro / Jie Liu / Christine Yu / Caleigh M Azumaya / Bobby Brillantes / Inna Zilberleyb / Henry Chen / Mariam B Rafiqzada / Lyra Garcia Sanchez / Wolf- ...Authors: Christopher W Koo / Steven K Gore / Soo Y Ro / Jie Liu / Christine Yu / Caleigh M Azumaya / Bobby Brillantes / Inna Zilberleyb / Henry Chen / Mariam B Rafiqzada / Lyra Garcia Sanchez / Wolf-Dietrich Heyer / Claudio Ciferri / Stanislau Yatskevich / ![]() Abstract: Homologous recombination (HR) is an important DNA repair pathway that safeguards genome integrity. During HR, the Rad51 nucleoprotein filaments catalyze strand invasion into a homologous duplex DNA. ...Homologous recombination (HR) is an important DNA repair pathway that safeguards genome integrity. During HR, the Rad51 nucleoprotein filaments catalyze strand invasion into a homologous duplex DNA. Filament formation requires a conserved family of Rad51 paralogs that act as tumor suppressors in humans. By capturing six distinct states using cryo-electron microscopy, we reveal that the Saccharomyces cerevisiae Rad51 paralog complex, composed of the Rad55-Rad57 heterodimer and the SHU (Psy3-Csm2-Shu1-Shu2) complex, selectively brings Rad51 to single-stranded DNA to seed filament formation. Rad51 itself is a transient yet integral component of this machinery which binds along the Rad57 subunit to complete a high-affinity DNA-binding site. We also uncover a dual-nucleotide regulatory mechanism: a structural ADP molecule stabilizes the complex, while a second, catalytic ATPase site at the Rad57-Rad51 interface promotes the release of the paralog complex. These structural and mechanistic features provide a blueprint for understanding the function of Rad51 paralogs across eukaryotes. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_72163.map.gz | 122.4 MB | EMDB map data format | |
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| Header (meta data) | emd-72163-v30.xml emd-72163.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72163_fsc.xml | 13.3 KB | Display | FSC data file |
| Images | emd_72163.png | 48.1 KB | ||
| Masks | emd_72163_msk_1.map | 244.1 MB | Mask map | |
| Filedesc metadata | emd-72163.cif.gz | 8.5 KB | ||
| Others | emd_72163_half_map_1.map.gz emd_72163_half_map_2.map.gz | 226.8 MB 226.8 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-72163 ftp://data.pdbj.org/pub/emdb/structures/EMD-72163 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9q2fMC ![]() 9q2cC ![]() 9q2eC ![]() 9q2hC ![]() 9q2iC ![]() 9q2lC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_72163.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | consensus | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.90625 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_72163_msk_1.map | ||||||||||||
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-Half map: half B
| File | emd_72163_half_map_1.map | ||||||||||||
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| Annotation | half B | ||||||||||||
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| Density Histograms |
-Half map: half A
| File | emd_72163_half_map_2.map | ||||||||||||
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| Annotation | half A | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
+Supramolecule #1: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
+Macromolecule #1: Methylated-DNA--protein-cysteine methyltransferase,DNA repair pro...
+Macromolecule #2: DNA repair protein RAD57
+Macromolecule #3: Chromosome segregation in meiosis protein 2
+Macromolecule #4: Platinum sensitivity protein 3
+Macromolecule #5: Suppressor of HU sensitivity involved in recombination protein 1
+Macromolecule #6: Suppressor of hydroxyurea sensitivity protein 2
+Macromolecule #7: DNA repair protein RAD51
+Macromolecule #8: ssDNA (9-mer)
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #12: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.2 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 56.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination 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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Trichoplusia ni (cabbage looper)

Processing
FIELD EMISSION GUN

