6YVD

Head segment of the S.cerevisiae condensin holocomplex in presence of ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.

Lee, B.G.Merkel, F.Allegretti, M.Hassler, M.Cawood, C.Lecomte, L.O'Reilly, F.J.Sinn, L.R.Gutierrez-Escribano, P.Kschonsak, M.Bravo, S.Nakane, T.Rappsilber, J.Aragon, L.Beck, M.Lowe, J.Haering, C.H.

(2020) Nat Struct Mol Biol 27: 743-751

  • DOI: https://doi.org/10.1038/s41594-020-0457-x
  • Primary Citation of Related Structures:  
    6YVD, 6YVU, 6YVV

  • PubMed Abstract: 

    Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Condensin complex subunit 2A [auth B]811Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRN1YBL097WYBL0830
UniProt
Find proteins for P38170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38170 
Go to UniProtKB:  P38170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38170
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Condensin complex subunit 3B [auth A]1,035Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YCG1YCS5YDR325W
UniProt
Find proteins for Q06680 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06680 
Go to UniProtKB:  Q06680
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06680
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 21,170Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMC2YFR031C
UniProt
Find proteins for P38989 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38989 
Go to UniProtKB:  P38989
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38989
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 41,478Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMC4YLR086WL9449.5
UniProt
Find proteins for Q12267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12267 
Go to UniProtKB:  Q12267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12267
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2015-CoG 681365

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references, Structure summary
  • Version 1.3: 2024-07-10
    Changes: Data collection