4UX3 | pdb_00004ux3

cohesin Smc3-HD:Scc1-N complex from yeast

• PDB DOI: https://doi.org/10.2210/pdb4UX3/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-18 Released: 2014-12-03 
• Deposition Author(s): Gligoris, T.G., Nasmyth, K., Lowe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.329 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.286 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Closing the Cohesin Ring: Structure and Function of its Smc3-Kleisin Interface.

Gligoris, T.G., Scheinost, J.C., Burmann, F., Petela, N., Chan, K., Uluocak, P., Beckouet, F., Gruber, S., Nasmyth, K., Lowe, J.

(2014) Science 346: 963

• PubMed: 25414305 
• DOI: https://doi.org/10.1126/science.1256917


• PubMed Abstract: 
  

  Through their association with a kleisin subunit (Scc1), cohesin's Smc1 and Smc3 subunits are thought to form tripartite rings that mediate sister chromatid cohesion. Unlike the structure of Smc1/Smc3 and Smc1/Scc1 interfaces, that of Smc3/Scc1 is not known. Disconnection of this interface is thought to release cohesin from chromosomes in a process regulated by acetylation. We show here that the N-terminal domain of yeast Scc1 contains two α helices, forming a four-helix bundle with the coiled coil emerging from Smc3's adenosine triphosphatase head. Mutations affecting this interaction compromise cohesin's association with chromosomes. The interface is far from Smc3 residues, whose acetylation prevents cohesin's dissociation from chromosomes. Cohesin complexes holding chromatids together in vivo do indeed have the configuration of hetero-trimeric rings, and sister DNAs are entrapped within these.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Max-Planck-Institut für Biochemie, 82152, Martinsried, Germany.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Medical Research Council (MRC) Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. [e-mail] [e-mail].
MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. [e-mail] [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: 76.11 kDa 
• Atom Count: 4,098 
• Modeled Residue Count: 507 
• Deposited Residue Count: 664 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3	A	543	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P47037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47037  Go to UniProtKB:  P47037

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOTIC CHROMOSOME DETERMINANT-RELATED PROTEIN	B	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12158 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12158  Go to UniProtKB:  Q12158

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	D [auth A]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.329 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.286 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.151	α = 90
b = 94.801	β = 90
c = 284.768	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Gligoris, T.G., Nasmyth, K., Lowe, J.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description