9YI6 | pdb_00009yi6

Cryo-EM structure of yeast Mgm101 bound to 83-mer ssDNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Mechanism of single-strand annealing from native mass spectrometry and cryo-EM structures of RAD52 homolog Mgm101.

Wheat, C.T.Qi, Z.Hussain, M.Zakharova, K.Wysocki, V.H.Bell, C.E.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.10.26.684629
  • Primary Citation of Related Structures:  
    9YI6, 9YI7, 9YI8, 9YI9, 9YIA

  • PubMed Abstract: 

    RAD52, the primary single-strand annealing (SSA) protein in humans, forms undecameric rings that bind ssDNA within a narrow, positively-charged groove. Whether RAD52 anneals two complementary ssDNAs on the same ring in cis , or between two ring-ssDNA complexes in trans , is unknown. Here, we determined cryo-EM structures of Mgm101, a RAD52 homolog from yeast mitochondria, in complexes with ssDNA, a duplex intermediate of annealing, and B-form dsDNA product. In all states, Mgm101 forms a closed nonadecameric ring that binds the backbone of the first ssDNA at the base of the narrow groove. The second complementary strand binds directly on top of the first to form an extended, unwound, and circular duplex intermediate of annealing. The third complex captures apparent B-form DNA product bound to a novel β-hairpin motif located on top of the Mgm101 ring, above the primary DNA-binding groove. Mass photometry and native mass spectrometry confirm and further elucidate the complexes formed in solution. Altogether, our data reveal the full SSA pathway of Mgm101 and suggest it anneals two complementary ssDNAs on the same ring in cis . Structural conservation with RAD52 suggests it is likely to use a similar cis mechanism of annealing.


  • Organizational Affiliation
    • Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial genome maintenance protein MGM101256Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MGM101MGM9YJR144WJ2181
UniProt
Find proteins for P32787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32787 
Go to UniProtKB:  P32787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32787
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
ssDNA (83-)T [auth Z]76Inovirus M13
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.2
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2212951

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references