+Open data
-Basic information
Entry | Database: PDB / ID: 6yuf | |||||||||
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Title | Cohesin complex with loader gripping DNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chromosome segregation Sister chromatid cohesion SMC complexes Cohesin ABC-ATPase Mis4-Scc2-NIPBL | |||||||||
Function / homology | Function and homology information pericentric heterochromatin => GO:0005721 / meiotic cohesin complex => GO:0030893 / mitotic cohesin dsDNA (leading strand) loading / positive regulation of mitotic cohesin loading / Cohesin Loading onto Chromatin / Resolution of Sister Chromatid Cohesion / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / : ...pericentric heterochromatin => GO:0005721 / meiotic cohesin complex => GO:0030893 / mitotic cohesin dsDNA (leading strand) loading / positive regulation of mitotic cohesin loading / Cohesin Loading onto Chromatin / Resolution of Sister Chromatid Cohesion / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / : / SUMOylation of DNA damage response and repair proteins / nucleus leading edge / SMC loading complex / mitotic telomere tethering at nuclear periphery / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / cohesin loader activity / heterochromatin island / maintenance of mitotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / chromosome, subtelomeric region / establishment of protein localization to chromatin / rDNA heterochromatin / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / condensed chromosome, centromeric region / sister chromatid cohesion / mitotic sister chromatid cohesion / nuclear chromosome / mitotic sister chromatid segregation / pericentric heterochromatin / enzyme regulator activity / chromosome / double-strand break repair / double-stranded DNA binding / single-stranded DNA binding / cell division / chromatin binding / DNA damage response / chromatin / DNA binding / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å | |||||||||
Authors | Higashi, T.L. / Eickhoff, P. / Sousa, J.S. / Costa, A. / Uhlmann, F. | |||||||||
Funding support | 2items
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Citation | Journal: Mol Cell / Year: 2020 Title: A Structure-Based Mechanism for DNA Entry into the Cohesin Ring. Authors: Torahiko L Higashi / Patrik Eickhoff / Joana S Sousa / Julia Locke / Andrea Nans / Helen R Flynn / Ambrosius P Snijders / George Papageorgiou / Nicola O'Reilly / Zhuo A Chen / Francis J ...Authors: Torahiko L Higashi / Patrik Eickhoff / Joana S Sousa / Julia Locke / Andrea Nans / Helen R Flynn / Ambrosius P Snijders / George Papageorgiou / Nicola O'Reilly / Zhuo A Chen / Francis J O'Reilly / Juri Rappsilber / Alessandro Costa / Frank Uhlmann / Abstract: Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and ...Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and cryoelectron microscopy (cryo-EM) to visualize a cohesin loading intermediate in which DNA is locked between two gates that lead into the cohesin ring. Building on this structural framework, we design experiments to establish the order of events during cohesin loading. In an initial step, DNA traverses an N-terminal kleisin gate that is first opened upon ATP binding and then closed as the cohesin loader locks the DNA against the ATPase gate. ATP hydrolysis will lead to ATPase gate opening to complete DNA entry. Whether DNA loading is successful or results in loop extrusion might be dictated by a conserved kleisin N-terminal tail that guides the DNA through the kleisin gate. Our results establish the molecular basis for cohesin loading onto DNA. | |||||||||
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 | 6yuf.cif.gz | 498.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yuf.ent.gz | 365.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yuf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6yuf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6yuf_validation.xml.gz | 79.8 KB | Display | |
Data in CIF | 6yuf_validation.cif.gz | 116.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yuf ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yuf | HTTPS FTP |
-Related structure data
Related structure data | 10930MC 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
-Protein , 2 types, 2 molecules BD
#1: Protein | Mass: 67913.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: rad21, SPCC338.17c / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30776 |
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#2: Protein | Mass: 180924.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: mis4, SPAC31A2.05c / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09725 |
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AC
#3: Protein | Mass: 140728.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: psm1, smc1, SPBC29A10.04 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O94383 |
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#4: Protein | Mass: 137048.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: psm3, smc3, SPAC10F6.09c / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O42649 |
-DNA chain , 2 types, 2 molecules XY
#5: DNA chain | Mass: 9852.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 9829.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 4 molecules
#7: Chemical | #8: Chemical | |
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-Details
Has ligand of interest | N |
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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 (natural) |
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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: 33.8 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 883184 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255148 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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