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- PDB-7ogt: Folded elbow of cohesin -

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Basic information

Entry
Database: PDB / ID: 7ogt
TitleFolded elbow of cohesin
Components
  • Structural maintenance of chromosomes protein 1
  • Structural maintenance of chromosomes protein 3
KeywordsCELL 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 / cohesin loader activity / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / DNA secondary structure binding / cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / cohesin loader activity / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / DNA secondary structure binding / 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 / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / 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
Smc1, ATP-binding cassette domain / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsLee, B.-G. / Gonzalez Llamazares, A. / Collier, J. / Patele, N.J. / Nasmyth, K.A. / Lowe, J.
CitationJournal: 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
DepositionMay 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 1
B: Structural maintenance of chromosomes protein 3


Theoretical massNumber of molelcules
Total (without water)283,0322
Polymers283,0322
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4290 Å2
ΔGint-25 kcal/mol
Surface area79550 Å2
MethodPISA

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Components

#1: Protein Structural maintenance of chromosomes protein 1 / DA-box protein SMC1


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 Structural maintenance of chromosomes protein 3 / DA-box protein SMC3


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cohesin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63892 / Symmetry type: POINT

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