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Open data
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Basic information
Entry | Database: PDB / ID: 6zz6 | |||||||||
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Title | Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex | |||||||||
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![]() | CELL CYCLE / SMC / cohesin / DNA | |||||||||
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 / establishment of meiotic sister chromatid cohesion / cohesin complex ...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 / establishment of meiotic sister chromatid cohesion / cohesin complex / DNA secondary structure binding / mitotic 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 / mitotic sister chromatid segregation / minor groove of adenine-thymine-rich DNA binding / chromosome, centromeric region / protein localization to chromatin / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / double-strand break repair / regulation of gene expression / double-stranded DNA binding / sequence-specific DNA binding / cell division / DNA damage response / chromatin binding / chromatin / apoptotic process / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Lee, B.-G. / Gonzalez Llamazares, A. / Collier, J. / Nasmyth, K.A. / Lowe, J. | |||||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 391.4 KB | Display | ![]() |
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PDB format | ![]() | 301.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11585MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 40854.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044- ...Details: 2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224,2-71, 87-195, 1044-1224 Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SMC1, CHL10, YFL008W / Production host: ![]() ![]() |
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#2: Protein | Mass: 48295.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, ...Details: 0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222,0-224, 997-1071,1104-1222 Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SMC3, YJL074C, J1049 / Production host: ![]() ![]() |
-Sister chromatid cohesion protein ... , 2 types, 2 molecules CD
#3: Protein | Mass: 9123.593 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502- ...Details: 67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555,67-103, 502-510, 519-555 Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: ![]() ![]() |
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#4: Protein | Mass: 171310.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SCC2, YDR180W, YD9395.14 / Production host: ![]() ![]() |
-DNA chain , 2 types, 2 molecules FG
#5: DNA chain | Mass: 10604.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 10297.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 4 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#7: Chemical | #8: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 0.485 MDa / Experimental value: YES | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 100 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / 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 | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: EPU / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 588164 / Symmetry type: POINT |