4RSJ | pdb_00004rsj

Pyrococcus furiosus Smc hinge domain with an extended coiled coil

• PDB DOI: https://doi.org/10.2210/pdb4RSJ/pdb

• Classification: CELL CYCLE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-08 Released: 2014-12-31 
• Deposition Author(s): Soh, Y.M., Shin, H.C., Oh, B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.251 (DCC) 

Starting Model: experimental

Literature

Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding.

Soh, Y.M., Burmann, F., Shin, H.C., Oda, T., Jin, K.S., Toseland, C.P., Kim, C., Lee, H., Kim, S.J., Kong, M.S., Durand-Diebold, M.L., Kim, Y.G., Kim, H.M., Lee, N.K., Sato, M., Oh, B.H., Gruber, S.

(2015) Mol Cell 57: 290-303

• PubMed: 25557547 
• DOI: https://doi.org/10.1016/j.molcel.2014.11.023
• Primary Citation Related Structures: 
  4RSI, 4RSJ


• PubMed Abstract: 
  

  SMC condensin complexes are central modulators of chromosome superstructure in all branches of life. Their SMC subunits form a long intramolecular coiled coil, which connects a constitutive "hinge" dimerization domain with an ATP-regulated "head" dimerization module. Here, we address the structural arrangement of the long coiled coils in SMC complexes. We unequivocally show that prokaryotic Smc-ScpAB, eukaryotic condensin, and possibly also cohesin form rod-like structures, with their coiled coils being closely juxtaposed and accurately anchored to the hinge. Upon ATP-induced binding of DNA to the hinge, however, Smc switches to a more open configuration. Our data suggest that a long-distance structural transition is transmitted from the Smc head domains to regulate Smc-ScpAB's association with DNA. These findings uncover a conserved architectural theme in SMC complexes, provide a mechanistic basis for Smc's dynamic engagement with chromosomes, and offer a molecular explanation for defects in Cornelia de Lange syndrome.

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Organizational Affiliation: 
• Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea.
Department of Physics, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.
Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea. Electronic address: [e-mail].
Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.44 kDa 
• Atom Count: 7,715 
• Modeled Residue Count: 1,064 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein Smc	A, B, C, D	276	Pyrococcus furiosus DSM 3638	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.284 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.251 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.923	α = 90
b = 116.882	β = 90
c = 145.493	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Soh, Y.M., Shin, H.C., Oh, B.H.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description