6BZF

Structure of S. cerevisiae Zip2:Spo16 complex, C2 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding.

Arora, K.Corbett, K.D.

(2019) Nucleic Acids Res 47: 2365-2376

  • DOI: https://doi.org/10.1093/nar/gky1273
  • Primary Citation of Related Structures:  
    6BZF, 6BZG

  • PubMed Abstract: 

    In eukaryotic meiosis, generation of haploid gametes depends on the formation of inter-homolog crossovers, which enable the pairing, physical linkage, and eventual segregation of homologs in the meiosis I division. A class of conserved meiosis-specific proteins, collectively termed ZMMs, are required for formation and spatial control of crossovers throughout eukaryotes. Here, we show that three Saccharomyces cerevisiae ZMM proteins-Zip2, Zip4 and Spo16-interact with one another and form a DNA-binding complex critical for crossover formation and control. We determined the crystal structure of a Zip2:Spo16 subcomplex, revealing a heterodimer structurally related to the XPF:ERCC1 endonuclease complex. Zip2:Spo16 lacks an endonuclease active site, but binds specific DNA structures found in early meiotic recombination intermediates. Mutations in multiple DNA-binding surfaces on Zip2:Spo16 severely compromise DNA binding, supporting a model in which the complex's central and HhH domains cooperate to bind DNA. Overall, our data support a model in which the Zip2:Zip4:Spo16 complex binds and stabilizes early meiotic recombination intermediates, then coordinates additional factors to promote crossover formation and license downstream events including synaptonemal complex assembly.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sporulation-specific protein 16
A, E
216Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPO16
UniProt
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17122 
Go to UniProtKB:  P17122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17122
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ZIP2206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
UniProt
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53061 
Go to UniProtKB:  P53061
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UniProt GroupP53061
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sporulation-specific protein 16
C, G
216Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPO16
UniProt
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P17122
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UniProt GroupP17122
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ZIP2206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
UniProt
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53061
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ZIP2
F, H
206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
UniProt
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53061 
Go to UniProtKB:  P53061
Entity Groups  
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UniProt GroupP53061
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, E
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
M0H
Query on M0H
B
L-PEPTIDE LINKINGC4 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.402α = 90
b = 63.589β = 90.6
c = 199.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM104141

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations