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- EMDB-72249: Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-72249
TitleRad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Composite map
Map data
Sample
  • Complex: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
    • Complex: Rad55-Rad57-SHU-Rad51-Rad51
    • Complex: ssDNA
KeywordsHomologous Recombination Complex / Rad51 Paralog Complex / DNA BINDING PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsYatskevich S / Koo CW / Ciferri C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2026
Title: 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.
History
DepositionAug 21, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72249.png

Downloads & links

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Map

FileDownload / File: emd_72249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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 EMDB: 0.005
Minimum - Maximum-0.005535541 - 0.03304909
Average (Standard dev.)0.00030613787 (±0.00061801675)
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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Sample components

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Entire : Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA

EntireName: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
Components
  • Complex: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
    • Complex: Rad55-Rad57-SHU-Rad51-Rad51
    • Complex: ssDNA

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Supramolecule #1: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA

SupramoleculeName: Rad55-Rad57-SHU-Rad51-Rad51 bound to AMP-PNP and ssDNA
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 271.98 KDa

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Supramolecule #2: Rad55-Rad57-SHU-Rad51-Rad51

SupramoleculeName: Rad55-Rad57-SHU-Rad51-Rad51 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: ssDNA

SupramoleculeName: ssDNA / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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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: 56.0 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 11289
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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