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Yorodumi- EMDB-10954: Condensin complex from S.cerevisiae ATP-free apo bridged state: o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10954 | ||||||||||||
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Title | Condensin complex from S.cerevisiae ATP-free apo bridged state: overall map | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | ||||||||||||
Authors | Lee B-G / Cawood C / Gutierrez-Escribano P / Nakane T / Merkel F / Hassler M / Haering CH / Aragon L / Lowe J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism. Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol ...Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol Bravo / Takanori Nakane / Juri Rappsilber / Luis Aragon / Martin Beck / Jan Löwe / Christian H Haering / Abstract: Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The ...Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10954.map.gz | 186.8 MB | EMDB map data format | |
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Header (meta data) | emd-10954-v30.xml emd-10954.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_10954.png | 47.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10954 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10954 | HTTPS FTP |
-Validation report
Summary document | emd_10954_validation.pdf.gz | 247.1 KB | Display | EMDB validaton report |
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Full document | emd_10954_full_validation.pdf.gz | 246.3 KB | Display | |
Data in XML | emd_10954_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10954 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10954 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10954.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Condensin
Entire | Name: Condensin |
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Components |
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-Supramolecule #1: Condensin
Supramolecule | Name: Condensin / type: complex / ID: 1 / Parent: 0 Details: complex of 5 protein subunits: Smc2; Smc4; Brn1; Ycs4; Ycg1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 500 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 / Component - Name: Tris |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10000 / Average exposure time: 10.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |