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 1.4 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: 10.1093/nar/gky1273
  • Primary Citation of Related Structures:  
    6BZG, 6BZF

  • 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-specif ...

    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.


    Related Citations: 
    • Structure of Zip2:Spo16, a conserved XPF:ERCC1-like complex critical for meiotic crossover formation
      Arora, K., Corbett, K.D.
      (2018) Biorxiv --: --

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sporulation-specific protein 16AE216Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPO16
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17122 
Go to UniProtKB:  P17122
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ZIP2B206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53061 
Go to UniProtKB:  P53061
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sporulation-specific protein 16CG216Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPO16
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17122 
Go to UniProtKB:  P17122
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ZIP2D206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53061 
Go to UniProtKB:  P53061
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ZIP2FH206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53061 
Go to UniProtKB:  P53061
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A,EL-PEPTIDE LINKINGC8 H18 N2 O2LYS
M0H
Query on M0H
BL-PEPTIDE LINKINGC4 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/538 SBGrid
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 

  • 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