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- EMDB-11585: Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11585
TitleCryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex
Map data
SampleComplex of cohesin, Scc2, ATP and DNA
  • Complex of cohesin and Scc2
  • double strand DNA
  • (Structural maintenance of chromosomes protein ...) x 2
  • (Sister chromatid cohesion protein ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 2
Function / homology
Function and homology information


SMC loading complex / positive regulation of mitotic cohesin loading / Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / meiotic sister chromatid cohesion / tRNA gene clustering / Establishment of Sister Chromatid Cohesion / 2-micrometer plasmid partitioning / Resolution of Sister Chromatid Cohesion / nuclear meiotic cohesin complex ...SMC loading complex / positive regulation of mitotic cohesin loading / Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / meiotic sister chromatid cohesion / tRNA gene clustering / Establishment of Sister Chromatid Cohesion / 2-micrometer plasmid partitioning / Resolution of Sister Chromatid Cohesion / nuclear meiotic cohesin complex / nuclear mitotic cohesin complex / rDNA condensation / DNA secondary structure binding / cohesin complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / SUMOylation of DNA damage response and repair proteins / establishment of protein localization to chromatin / establishment of mitotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / synaptonemal complex assembly / synaptonemal complex / reciprocal meiotic recombination / mitotic chromosome condensation / mitotic sister chromatid cohesion / sister chromatid cohesion / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / protein acetylation / 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 / chromatin / cellular response to DNA damage stimulus / apoptotic process / chromatin binding / protein kinase binding / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Sister chromatid cohesion C-terminal domain / Sister chromatid cohesion C-terminus / Scc2/Nipped-B family / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein, C-terminal, eukaryotic / N terminus of Rad21 / Rec8 like protein / Conserved region of Rad21 / Rec8 like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic ...Sister chromatid cohesion C-terminal domain / Sister chromatid cohesion C-terminus / Scc2/Nipped-B family / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein, C-terminal, eukaryotic / N terminus of Rad21 / Rec8 like protein / Conserved region of Rad21 / Rec8 like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / HEAT repeat associated with sister chromatid cohesion / HEAT repeat associated with sister chromatid cohesion protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / SMCs flexible hinge superfamily / SMCs flexible hinge / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 1 / Structural maintenance of chromosomes protein 3 / Sister chromatid cohesion protein 2 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLee B-G / Gonzalez Llamazares A / Collier J / Nasmyth KA / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
CitationJournal: Elife / Year: 2020
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
DepositionAug 4, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6zz6
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11585.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å
1.07 Å/pix.
x 320 pix.
= 342.4 Å
1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.02
Minimum - Maximum-0.087005906 - 0.17313385
Average (Standard dev.)0.0001588921 (±0.0025428992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0870.1730.000

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Supplemental data

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Segmentation: #1

Fileemd_11585_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_11585_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_11585_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of cohesin, Scc2, ATP and DNA

EntireName: Complex of cohesin, Scc2, ATP and DNA / Number of Components: 11

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Component #1: protein, Complex of cohesin, Scc2, ATP and DNA

ProteinName: Complex of cohesin, Scc2, ATP and DNA / Recombinant expression: No
MassExperimental: 485 kDa

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Component #2: protein, Complex of cohesin and Scc2

ProteinName: Complex of cohesin and Scc2 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, double strand DNA

ProteinName: double strand DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Structural maintenance of chromosomes protein 1,Structur...

ProteinName: Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.8545 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: protein, Structural maintenance of chromosomes protein 3,Structur...

ProteinName: Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.295016 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, Sister chromatid cohesion protein 1,Sister chromatid coh...

ProteinName: Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.123593 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #7: protein, Sister chromatid cohesion protein 2

ProteinName: Sister chromatid cohesion protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 171.310625 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #8: nucleic-acid, DNA (34-MER)

nucleic acidName: DNA (34-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)
MassTheoretical: 10.604072 kDa
SourceSpecies: synthetic construct (others)

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Component #9: nucleic-acid, DNA (34-MER)

nucleic acidName: DNA (34-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)
MassTheoretical: 10.297598 kDa
SourceSpecies: synthetic construct (others)

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Component #10: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #11: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 100 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 55 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 588164
3D reconstructionResolution: 3.4 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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