5XG3

Crystal structure of the ATPgS-engaged Smc head domain with an extended coiled coil bound to the C-terminal domain of ScpA derived from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization

Diebold-Durand, M.L.Lee, H.Ruiz Avila, L.B.Noh, H.Shin, H.C.Im, H.Bock, F.P.Burmann, F.Durand, A.Basfeld, A.Ham, S.Basquin, J.Oh, B.-H.Gruber, S.

(2017) Mol Cell 67: 334-347.e5

  • DOI: https://doi.org/10.1016/j.molcel.2017.06.010
  • Primary Citation of Related Structures:  
    5NMO, 5NNV, 5XEI, 5XG2, 5XG3, 5XNS

  • PubMed Abstract: 

    Multi-subunit SMC complexes control chromosome superstructure and promote chromosome disjunction, conceivably by actively translocating along DNA double helices. SMC subunits comprise an ABC ATPase "head" and a "hinge" dimerization domain connected by a 49 nm coiled-coil "arm." The heads undergo ATP-dependent engagement and disengagement to drive SMC action on the chromosome. Here, we elucidate the architecture of prokaryotic Smc dimers by high-throughput cysteine cross-linking and crystallography. Co-alignment of the Smc arms tightly closes the interarm space and misaligns the Smc head domains at the end of the rod by close apposition of their ABC signature motifs. Sandwiching of ATP molecules between Smc heads requires them to substantially tilt and translate relative to each other, thereby opening up the Smc arms. We show that this mechanochemical gating reaction regulates chromosome targeting and propose a mechanism for DNA translocation based on the merging of DNA loops upon closure of Smc arms.


  • Organizational Affiliation

    Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein Smc
A, B
435Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: smcylqABSU15940
UniProt
Find proteins for P51834 (Bacillus subtilis (strain 168))
Explore P51834 
Go to UniProtKB:  P51834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51834
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Segregation and condensation protein A
C, D
89Bacillus subtilisMutation(s): 0 
Gene Names: scpASAMN05878487_2386
UniProt
Find proteins for P35154 (Bacillus subtilis (strain 168))
Explore P35154 
Go to UniProtKB:  P35154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35154
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.103α = 90
b = 104.783β = 90
c = 185.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description