+Open data
-Basic information
Entry | Database: PDB / ID: 6qpw | ||||||
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Title | Structural basis of cohesin ring opening | ||||||
Components |
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Keywords | CELL CYCLE / Chromatin / genome segregation / cohesin | ||||||
Function / homology | Function and homology information Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / synaptonemal complex assembly / meiotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / synaptonemal complex assembly / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / double-strand break repair / mitotic cell cycle / double-stranded DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Panne, D. / Muir, K.W. / Li, Y. / Weis, F. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qpw.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qpw.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qpw_validation.pdf.gz | 863.4 KB | Display | wwPDB validaton report |
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Full document | 6qpw_full_validation.pdf.gz | 869.9 KB | Display | |
Data in XML | 6qpw_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 6qpw_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qpw ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qpw | HTTPS FTP |
-Related structure data
Related structure data | 4616MC 6qpqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Structural maintenance of chromosomes ... , 2 types, 2 molecules AC
#1: Protein | Mass: 27570.475 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) / References: UniProt: G0SGH3 |
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#3: Protein | Mass: 61051.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SMC3, YJL074C, J1049 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47037 |
-Sister chromatid cohesion protein ... , 2 types, 2 molecules BE
#2: Protein | Mass: 9489.940 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) / References: UniProt: Q12158 |
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#4: Protein | Mass: 42292.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04, CTHT_0066330 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12158, UniProt: G0SGH3 |
-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42.08 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178162 / Symmetry type: POINT |