8URQ

Spo11 core complex with gapped DNA

• PDB DOI: https://doi.org/10.2210/pdb8URQ/pdb
• EM Map EMD-42497: EMDB EMDataResource
• NAKB: 8URQ

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-10-26 Released: 2024-06-26 
• Deposition Author(s): Yu, Y., Patel, D.J.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

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

Literature

Cryo-EM structure of the yeast Spo11 core complex bound to DNA

Yu, Y., Wang, J.C., Liu, K.X., Zheng, Z., Patel, D.J., Keeney, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 167.33 kDa 
• Atom Count: 8,569 
• Modelled Residue Count: 1,024 
• Deposited Residue Count: 1,349 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic recombination protein REC104	A [auth F]	182	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: REC104, YHR157W
UniProt
Find proteins for P33323 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33323  Go to UniProtKB:  P33323

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic recombination protein REC102	B	264	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: REC102, YLR329W, L8543.17
UniProt
Find proteins for Q02721 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02721  Go to UniProtKB:  Q02721

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiosis-specific protein SPO11	C [auth A]	435	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SPO11
UniProt
Find proteins for P23179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23179  Go to UniProtKB:  P23179

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiviral protein SKI8	D [auth C]	397	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SKI8
UniProt
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02793  Go to UniProtKB:  Q02793

Entity ID: 5
Molecule	Chains	Length	Organism	Image
gapped DNA	E [auth D]	71	Saccharomyces cerevisiae S288C

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Yu, Y., Patel, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R01 HD110120

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release