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Yorodumi- EMDB-13785: Cryo-EM map of clamped S.cerevisiae condensin-DNA complex (pentam... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13785 | ||||||||||||
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Title | Cryo-EM map of clamped S.cerevisiae condensin-DNA complex (pentamer dataset) | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | condensin / SMC / CELL CYCLE | ||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 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_13785.map.gz | 14.9 MB | EMDB map data format | |
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Header (meta data) | emd-13785-v30.xml emd-13785.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_13785.png | 30.1 KB | ||
Filedesc metadata | emd-13785.cif.gz | 3.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13785 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13785.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: 1.08 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 tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
Entire | Name: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3 |
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Components |
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-Supramolecule #1: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3
Supramolecule | Name: complex of condensin tetamer (smc2, smc4, brn1, ycs4), DNA, ADP-BeF3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 515 kDa/nm |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45112 |
-Atomic model buiding 1
Refinement | Space: REAL |
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