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Yorodumi- EMDB-13783: Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13783 | ||||||||||||
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Title | Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (Form I) | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy ...negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy / synaptonemal complex assembly / condensed chromosome, centromeric region / mitotic chromosome condensation / chromosome condensation / silent mating-type cassette heterochromatin formation / mitotic sister chromatid segregation / minor groove of adenine-thymine-rich DNA binding / 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 S288C (yeast) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Lee B-G / Rhodes J / Lowe J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Clamping of DNA shuts the condensin neck gate. Authors: Byung-Gil Lee / James Rhodes / Jan Löwe / Abstract: SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex ...SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolyzed. The DNA is clamped within a compartment that has been reported previously in other structural maintenance of chromosomes (SMC) complexes, including Rad50, cohesin, and MukBEF. With the caveat of important differences, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolyzing ATP and translocating DNA. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13783.map.gz | 14.7 MB | EMDB map data format | |
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Header (meta data) | emd-13783-v30.xml emd-13783.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
Images | emd_13783.png | 126.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13783 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13783 | HTTPS FTP |
-Validation report
Summary document | emd_13783_validation.pdf.gz | 317.4 KB | Display | EMDB validaton report |
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Full document | emd_13783_full_validation.pdf.gz | 317 KB | Display | |
Data in XML | emd_13783_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_13783_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13783 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13783 | HTTPS FTP |
-Related structure data
Related structure data | 7q2xMC 7q2yC 7q2zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13783.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : complex of condensin tetramer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
+Supramolecule #1: complex of condensin tetramer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
+Macromolecule #1: Structural maintenance of chromosomes protein 2
+Macromolecule #2: Structural maintenance of chromosomes protein 4
+Macromolecule #3: Condensin complex subunit 2
+Macromolecule #4: Condensin complex subunit 1
+Macromolecule #5: DNA (36-MER)
+Macromolecule #6: DNA (36-MER)
+Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #8: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 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 |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 286294 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |