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 9Q2E | pdb_00009q2e

Rad55-Rad57-SHU bound to ssDNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Q2E

This is version 1.2 of the entry. See complete history. 

Literature

Yeast Rad55-Rad57-SHU paralog complex dynamically promotes Rad51 filament formation.

Koo, C.W., Gore, S.K., Ro, S.Y., Liu, J., Yu, C., Azumaya, C.M., Brillantes, B., Zilberleyb, I., Chen, H., Rafiqzada, M.B., Garcia Sanchez, L., Heyer, W.D., Ciferri, C., Yatskevich, S.

(2026) Mol Cell 86: 3639

  • DOI: https://doi.org/10.1016/j.molcel.2026.06.045
  • Primary Citation Related Structures: 
    9Q2C, 9Q2E, 9Q2F, 9Q2H, 9Q2I, 9Q2L

  • PubMed 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. 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.


  • Organizational Affiliation: 
    • Protein Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 229.54 kDa 
  • Atom Count: 11,538 
  • Modeled Residue Count: 1,407 
  • Deposited Residue Count: 2,003 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferase,DNA repair protein RAD55631Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.1.1.63
UniProt
Find proteins for E5BBQ0 (Homo sapiens)
Explore E5BBQ0 
Go to UniProtKB:  E5BBQ0
Find proteins for P38953 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38953 
Go to UniProtKB:  P38953
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE5BBQ0P38953
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein RAD57460Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD57, YDR004W, YD8119.10
UniProt
Find proteins for P25301 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25301 
Go to UniProtKB:  P25301
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UniProt GroupP25301
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromosome segregation in meiosis protein 2213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSM2, YIL132C
UniProt
Find proteins for P40465 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40465 
Go to UniProtKB:  P40465
Entity Groups
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UniProt GroupP40465
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Platinum sensitivity protein 3281Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSY3, YLR376C, L8039.17
UniProt
Find proteins for Q12318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12318 
Go to UniProtKB:  Q12318
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UniProt GroupQ12318
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Suppressor of HU sensitivity involved in recombination protein 1150Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SHU1, YHL006C
UniProt
Find proteins for P38751 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38751 
Go to UniProtKB:  P38751
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UniProt GroupP38751
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Suppressor of hydroxyurea sensitivity protein 2262Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SHU2, C1Q_04575
UniProt
Find proteins for C7GVQ9 (Saccharomyces cerevisiae (strain JAY291))
Explore C7GVQ9 
Go to UniProtKB:  C7GVQ9
Entity Groups
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UniProt GroupC7GVQ9
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 7
MoleculeChains LengthOrganismImage
ssDNA (6-mer)G [auth H]6Saccharomyces cerevisiae
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Data collection, Database references
  • Version 1.2: 2026-09-30
    Changes: Data collection, Database references