+Open data
-Basic information
Entry | Database: PDB / ID: 6yvv | ||||||||||||
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Title | Condensin complex from S.cerevisiae ATP-free apo bridged state | ||||||||||||
Components |
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Keywords | CELL CYCLE / essential for the functional organization of genomes | ||||||||||||
Function / homology | Function and homology information negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / synaptonemal complex assembly / nucleophagy / condensed chromosome, centromeric region / mitotic chromosome condensation / chromosome condensation / silent mating-type cassette heterochromatin formation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / condensed chromosome / histone binding / double-stranded DNA binding / cell division / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||||||||
Authors | Lee, B.-G. / Cawood, C. / Gutierrez-Escribano, P. / Nakane, T. / Merkel, F. / Hassler, M. / Haering, C.H. / Aragon, L. / Lowe, J. | ||||||||||||
Funding support | United Kingdom, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yvv.cif.gz | 409.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yvv.ent.gz | 296.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yvv_validation.pdf.gz | 840.2 KB | Display | wwPDB validaton report |
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Full document | 6yvv_full_validation.pdf.gz | 860.9 KB | Display | |
Data in XML | 6yvv_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6yvv_validation.cif.gz | 83.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/6yvv ftp://data.pdbj.org/pub/pdb/validation_reports/yv/6yvv | HTTPS FTP |
-Related structure data
Related structure data | 10952MC 6yvdC 6yvuC 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
#1: Protein | Mass: 134806.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SMC2, YFR031C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38989 |
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#2: Protein | Mass: 162435.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SMC4, YLR086W, L9449.5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12267 |
#3: Protein | Mass: 87940.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: BRN1, YBL097W, YBL0830 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38170 |
#4: Protein | Mass: 133882.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: YCS4, LOC7, YLR272C, L8479.14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06156 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Condensin / Type: COMPLEX Details: complex of 5 protein subunits: Smc2; Smc4; Brn1; Ycs4; Ycg1 Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 500 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Buffer component | Name: Tris |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 100 K |
-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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10000 |
EM imaging optics | Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24593 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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