4RSI | pdb_00004rsi

Yeast Smc2-Smc4 hinge domain with extended coiled coils

• PDB DOI: https://doi.org/10.2210/pdb4RSI/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• 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: 2.90 Å
• R-Value Free: 
  0.266 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.242 (DCC) 

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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 90.8 kDa 
• Atom Count: 5,252 
• Modeled Residue Count: 669 
• Deposited Residue Count: 794 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 2	A	397	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: Saccharomyces cerevisiae, SMC2, YFR031C
UniProt
Find proteins for P38989 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38989  Go to UniProtKB:  P38989

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 4	B	397	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: L9449.5, Saccharomyces cerevisiae, SMC4, YLR086W
UniProt
Find proteins for Q12267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12267  Go to UniProtKB:  Q12267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.266 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.242 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.259	α = 90
b = 49.707	β = 92.52
c = 154.283	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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: 2024-02-28
  Changes: Data collection, Database references, Derived calculations