6BZF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.286 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 

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:  

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sporulation-specific protein 16
A, E
216Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPO16
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein ZIP2
B
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53061
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sporulation-specific protein 16
C, G
216Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPO16
Find proteins for P17122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein ZIP2
D
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53061
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Protein ZIP2
F, H
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ZIP2
Find proteins for P53061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53061
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
M0H
Query on M0H
B, D, F, H
L-PEPTIDE LINKINGC4 H9 N O3 SCYS
MLY
Query on MLY
A, B, D, E, F, H
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.286 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/538 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 169.402α = 90.00
b = 63.589β = 90.60
c = 199.043γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Data collection, Database references
  • Version 1.3: 2019-03-27
    Type: Data collection, Database references
  • Version 1.4: 2020-01-01
    Type: Author supporting evidence