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- PDB-6h8q: Structural basis for Scc3-dependent cohesin recruitment to chromatin -

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Basic information

Entry
Database: PDB / ID: 6h8q
TitleStructural basis for Scc3-dependent cohesin recruitment to chromatin
Components
  • (DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)- ...) x 3
  • Cohesin subunit SCC3
  • DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
  • Sister chromatid cohesion protein 1
KeywordsCELL CYCLE / Cohesin cell proliferation Scc3 DNA binding
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / chromosome segregation / G2/M transition of mitotic cell cycle / double-strand break repair / cell division / DNA damage response / chromatin binding / apoptotic process / chromatin / protein kinase binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Cohesin subunit SCC3, C-terminal domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal ...: / Cohesin subunit SCC3, C-terminal domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Cohesin subunit SCC3 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.631 Å
AuthorsLi, Y. / Muir, K. / Panne, D.
CitationJournal: Elife / Year: 2018
Title: Structural basis for Scc3-dependent cohesin recruitment to chromatin.
Authors: Li, Y. / Muir, K. / Bowler, M.W. / Metz, J. / Haering, C.H. / Panne, D.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cohesin subunit SCC3
B: Cohesin subunit SCC3
G: Sister chromatid cohesion protein 1
H: Sister chromatid cohesion protein 1
E: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
C: DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)312,8078
Polymers312,8078
Non-polymers00
Water00
1
A: Cohesin subunit SCC3
G: Sister chromatid cohesion protein 1
E: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)156,4044
Polymers156,4044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-37 kcal/mol
Surface area53700 Å2
MethodPISA
2
B: Cohesin subunit SCC3
H: Sister chromatid cohesion protein 1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)156,4034
Polymers156,4034
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-43 kcal/mol
Surface area53760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)296.240, 110.020, 115.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABGH

#1: Protein Cohesin subunit SCC3 / Irregular cell behavior protein 1


Mass: 133172.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: IRR1, SCC3, YIL026C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P40541
#2: Protein Sister chromatid cohesion protein 1


Mass: 11583.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCD1, PDS3, RHC21, SCC1, YDL003W, YD8119.04 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q12158

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DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)- ... , 3 types, 3 molecules EFD

#3: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5861.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5785.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (5'-D(P*CP*TP*TP*TP*CP*GP*TP*TP*TP*CP*CP*TP*TP*GP*AP*AP*AP*AP*A)-3')


Mass: 5769.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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DNA chain , 1 types, 1 molecules C

#5: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*CP*AP*AP*GP*GP*AP*AP*AP*CP*GP*AP*AP*AP*G)-3')


Mass: 5876.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 10% PEG 8000, 0.1M Bis-TRIS, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 20963 / % possible obs: 91.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.9
Reflection shellResolution: 3.6→3.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UVK, 4UVL

4uvk

4uvl


Resolution: 3.631→50 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 50.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3185 1093 5.22 %
Rwork0.2835 --
obs0.2854 20930 48.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.631→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14805 1558 0 0 16363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216842
X-RAY DIFFRACTIONf_angle_d0.45123076
X-RAY DIFFRACTIONf_dihedral_angle_d15.1519925
X-RAY DIFFRACTIONf_chiral_restr0.0342683
X-RAY DIFFRACTIONf_plane_restr0.0032610

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