5OQR | pdb_00005oqr

Crystal structure of the S. pombe condensin Cnd3-Cnd2 subcomplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5OQR

This is version 1.2 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: https://doi.org/10.1016/j.cell.2017.09.008
  • Primary Citation Related Structures: 
    5OQN, 5OQO, 5OQP, 5OQQ, 5OQR

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 212.84 kDa 
  • Atom Count: 13,032 
  • Modeled Residue Count: 1,597 
  • Deposited Residue Count: 1,846 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Condensin complex subunit 3
A, B
788Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cnd3SPCC188.03
UniProt
Find proteins for Q10429 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q10429 
Go to UniProtKB:  Q10429
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10429
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Condensin complex subunit 2
C, D
135Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cnd2SPCC306.03c
UniProt
Find proteins for Q9Y7R3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y7R3 
Go to UniProtKB:  Q9Y7R3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y7R3
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.407α = 90
b = 142.113β = 90
c = 176.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references