8URQ

Spo11 core complex with gapped DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of the Spo11 core complex bound to DNA.

Yu, Y.Wang, J.Liu, K.Zheng, Z.Arter, M.Claeys Bouuaert, C.Pu, S.Patel, D.J.Keeney, S.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01382-8
  • Primary Citation of Related Structures:  
    8URQ, 8URU

  • PubMed Abstract: 

    DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data have not been available, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-electron microscopy structures at up to 3.3-Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104 and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3'-OH and first 5' overhanging nucleotide, establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiotic recombination protein REC104A [auth F]182Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: REC104YHR157W
UniProt
Find proteins for P33323 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P33323
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UniProt GroupP33323
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Meiotic recombination protein REC102264Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: REC102YLR329WL8543.17
UniProt
Find proteins for Q02721 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02721
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UniProt GroupQ02721
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Meiosis-specific protein SPO11C [auth A]435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPO11
EC: 5.6.2.2
UniProt
Find proteins for P23179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P23179
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UniProt GroupP23179
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral protein SKI8D [auth C]397Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI8
UniProt
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02793 
Go to UniProtKB:  Q02793
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UniProt GroupQ02793
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Entity ID: 5
MoleculeChains LengthOrganismImage
gapped DNAE [auth D]71Saccharomyces cerevisiae S288C
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01 HD110120

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary