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 

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, 5OQR, 5OQN, 5OQQ

  • 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 unde ...

    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 Ycg1Cnd3 HEAT-repeat and Brn1Cnd2 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), Meyerhofstra├če 1, 69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Condensin complex subunit 3
A
871Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YCG1 (YCS5)
Find proteins for Q06680 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06680
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Condensin complex subunit 2
B
152Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BRN1
Find proteins for P38170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38170
Entity ID: 3
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.803α = 90.00
b = 117.940β = 90.00
c = 154.968γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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