5OQO

Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex bound to DNA (crystal form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes.

Kschonsak, M.Merkel, F.Bisht, S.Metz, J.Rybin, V.Hassler, M.Haering, C.H.

(2017) Cell 171: 588-600.e24

  • DOI: 10.1016/j.cell.2017.09.008
  • Primary Citation of Related Structures:  
    5OQP, 5OQO, 5OQR, 5OQQ, 5OQN

  • PubMed Abstract: 
  • Condensin protein complexes coordinate the formation of mitotic chromosomes and thereby ensure the successful segregation of replicated genomes. Insights into how condensin complexes bind to chromosomes and alter their topology are essential for understanding the molecular principles behind the large-scale chromatin rearrangements that take place during cell divisions ...

    Condensin protein complexes coordinate the formation of mitotic chromosomes and thereby ensure the successful segregation of replicated genomes. Insights into how condensin complexes bind to chromosomes and alter their topology are essential for understanding the molecular principles behind the large-scale chromatin rearrangements that take place during cell divisions. Here, we identify a direct DNA-binding site in the eukaryotic condensin complex, which is formed by its Ycg1 Cnd3 HEAT-repeat and Brn1 Cnd2 kleisin subunits. DNA co-crystal structures reveal a conserved, positively charged groove that accommodates the DNA double helix. A peptide loop of the kleisin subunit encircles the bound DNA and, like a safety belt, prevents its dissociation. Firm closure of the kleisin loop around DNA is essential for the association of condensin complexes with chromosomes and their DNA-stimulated ATPase activity. Our data suggest a sophisticated molecular basis for anchoring condensin complexes to chromosomes that enables the formation of large-sized chromatin loops.


    Organizational Affiliation

    Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address: christian.haering@embl.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Condensin complex subunit 3 A871Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YCG1YCS5YDR325W
Find proteins for Q06680 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06680 
Go to UniProtKB:  Q06680
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Condensin complex subunit 2 B152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRN1YBL097WYBL0830
Find proteins for P38170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38170 
Go to UniProtKB:  P38170
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3')C, D18synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PGE
    Query on PGE

    Download Ideal Coordinates CCD File 
    A
    TRIETHYLENE GLYCOL
    C6 H14 O4
    ZIBGPFATKBEMQZ-UHFFFAOYSA-N
     Ligand Interaction
    TRS
    Query on TRS

    Download Ideal Coordinates CCD File 
    A
    2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    C4 H12 N O3
    LENZDBCJOHFCAS-UHFFFAOYSA-O
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.25 Å
    • R-Value Free: 0.273 
    • R-Value Work: 0.236 
    • R-Value Observed: 0.238 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 88.803α = 90
    b = 117.94β = 90
    c = 154.968γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    SCALAdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermany5853/2
    European Research CouncilERC-2015-CoG 681365

    Revision History  (Full details and data files)

    • Version 1.0: 2017-10-18
      Type: Initial release
    • Version 1.1: 2017-11-01
      Changes: Database references