5XNS

Crystal structure of the Smc head domain with an extended coiled coil bound to the C-terminal domain of ScpA derived from Pyrococcus furiosus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


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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: 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 ...

    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. Electronic address: stephan.gruber@unil.ch.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein SmcA405Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: smc, PF1843
UniProt
Find proteins for Q8TZY2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZY2 
Go to UniProtKB:  Q8TZY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZY2
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Segregation and condensation protein AB [auth C]74Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF1842
UniProt
Find proteins for Q8TZY3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZY3 
Go to UniProtKB:  Q8TZY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZY3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.304α = 90
b = 150.003β = 90
c = 51.081γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MR-Rosettaphasing
HKLdata reduction
HKLdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release