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- PDB-6qpq: The structure of the cohesin head module elucidates the mechanism... -

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Basic information

Entry
Database: PDB / ID: 6qpq
TitleThe structure of the cohesin head module elucidates the mechanism of ring opening
Components
  • Sister chromatid cohesion protein 1
  • Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
KeywordsCELL CYCLE / Cohesin / cell division / genome regulation / sister chromatid cohesion / SMC / kleisin
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / double-strand break repair / cell division / DNA damage response / chromatin binding / apoptotic process / protein kinase binding / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge ...Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Structural maintenance of chromosomes protein / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, Y. / Muir, K.W. / Panne, D.
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening.
Authors: Kyle W Muir / Yan Li / Felix Weis / Daniel Panne /
Abstract: Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring- ...Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
B: Sister chromatid cohesion protein 1
C: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
D: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)230,4724
Polymers230,4724
Non-polymers00
Water6,179343
1
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
B: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)115,2362
Polymers115,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-17 kcal/mol
Surface area24870 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
D: Sister chromatid cohesion protein 1


Theoretical massNumber of molelcules
Total (without water)115,2362
Polymers115,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-18 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.752, 111.130, 166.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein


Mass: 51883.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0066330 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGH3
#2: Protein Sister chromatid cohesion protein 1


Mass: 63352.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12158
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 30% PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→45.7 Å / Num. obs: 82453 / % possible obs: 98.8 % / Redundancy: 4.5 % / Net I/σ(I): 13.36
Reflection shellResolution: 2.14→2.27 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.7 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs84151 98.8 %
Refinement stepCycle: LAST / Resolution: 2.1→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 0 343 8091

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