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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11585 | |||||||||
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Title | Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex | |||||||||
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![]() | SMC / cohesin / DNA / CELL CYCLE | |||||||||
Function / homology | ![]() SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / tRNA gene clustering / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion ...SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / tRNA gene clustering / meiotic cohesin complex / cohesin loader activity / establishment of meiotic sister chromatid cohesion / DNA secondary structure binding / mitotic cohesin complex / cohesin complex / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / SUMOylation of DNA damage response and repair proteins / synaptonemal complex assembly / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / chromosome, centromeric region / protein localization to chromatin / condensed nuclear chromosome / double-strand break repair / regulation of gene expression / double-stranded DNA binding / sequence-specific DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / chromatin / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Lee B-G / Gonzalez Llamazares A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3. Authors: James E Collier / Byung-Gil Lee / Maurici Brunet Roig / Stanislav Yatskevich / Naomi J Petela / Jean Metson / Menelaos Voulgaris / Andres Gonzalez Llamazares / Jan Löwe / Kim A Nasmyth / ![]() Abstract: In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped ...In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are 'clamped' in a sub-compartment created by Scc2's association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
Images | ![]() | 147.5 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() | 98.5 MB 98.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 708.2 KB | Display | ![]() |
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Full document | ![]() | 707.8 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zz6MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
File | emd_11585_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11585_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Complex of cohesin, Scc2, ATP and DNA
+Supramolecule #1: Complex of cohesin, Scc2, ATP and DNA
+Supramolecule #2: Complex of cohesin and Scc2
+Supramolecule #3: double strand DNA
+Macromolecule #1: Structural maintenance of chromosomes protein 1,Structural mainte...
+Macromolecule #2: Structural maintenance of chromosomes protein 3,Structural mainte...
+Macromolecule #3: Sister chromatid cohesion protein 1,Sister chromatid cohesion pro...
+Macromolecule #4: Sister chromatid cohesion protein 2
+Macromolecule #5: DNA (34-MER)
+Macromolecule #6: DNA (34-MER)
+Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #8: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 588164 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |