+Open data
-Basic information
Entry | Database: PDB / ID: 7ogt | ||||||
---|---|---|---|---|---|---|---|
Title | Folded elbow of cohesin | ||||||
Components |
| ||||||
Keywords | CELL CYCLE / Cohesin / Elbow / Hinge / Smc1 / Smc3 / coiled coil / DNA | ||||||
Function / homology | Function and homology information Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / DNA secondary structure binding / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / DNA secondary structure binding / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / mitotic sister chromatid segregation / minor groove of adenine-thymine-rich DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair / double-stranded DNA binding / cell division / protein kinase binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||
Authors | Lee, B.-G. / Gonzalez Llamazares, A. / Collier, J. / Patele, N.J. / Nasmyth, K.A. / Lowe, J. | ||||||
Citation | Journal: Elife / Year: 2021 Title: Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes. Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier ...Authors: Naomi J Petela / Andres Gonzalez Llamazares / Sarah Dixon / Bin Hu / Byung-Gil Lee / Jean Metson / Heekyo Seo / Antonio Ferrer-Harding / Menelaos Voulgaris / Thomas Gligoris / James Collier / Byung-Ha Oh / Jan Löwe / Kim A Nasmyth / Abstract: Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 ...Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement of cohesin's Smc1 and Smc3 head domains. Scc2's replacement by Pds5 abrogates cohesin's ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1's ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin's coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation () within Smc1's hinge that alters how Scc2 and Pds5 interact with Smc1's hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin's hinge, which in turn requires coiled coil folding. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ogt.cif.gz | 239 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ogt.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ogt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ogt_validation.pdf.gz | 643.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ogt_full_validation.pdf.gz | 652.1 KB | Display | |
Data in XML | 7ogt_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 7ogt_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7ogt ftp://data.pdbj.org/pub/pdb/validation_reports/og/7ogt | HTTPS FTP |
-Related structure data
Related structure data | 12887MC 7dg5C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 141491.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SMC1, CHL10, YFL008W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32908 |
---|---|
#2: Protein | Mass: 141539.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SMC3, YJL074C, J1049 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47037 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cohesin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
-Processing
EM software | Name: EPU / Category: image acquisition |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63892 / Symmetry type: POINT |