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- PDB-5frs: Structure of the Pds5-Scc1 complex and implications for cohesin f... -

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Basic information

Entry
Database: PDB / ID: 5frs
TitleStructure of the Pds5-Scc1 complex and implications for cohesin function
Components
  • SISTER CHROMATID COHESION PROTEIN 1
  • SISTER CHROMATID COHESION PROTEIN PDS5
KeywordsCELL CYCLE / COHESIN / DNA REPLICATION / SISTER CHROMATID COHESION / PDS5 / SMC3 / SCC1 / SMC1 / WAPL
Function / homology
Function and homology information


meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / mitotic cohesin complex / cohesin complex / meiotic DNA double-strand break formation / SUMOylation of DNA damage response and repair proteins / homologous chromosome pairing at meiosis / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion ...meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / mitotic cohesin complex / cohesin complex / meiotic DNA double-strand break formation / SUMOylation of DNA damage response and repair proteins / homologous chromosome pairing at meiosis / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / mitotic chromosome condensation / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / meiotic cell cycle / condensed nuclear chromosome / double-strand break repair / cell division / apoptotic process / DNA damage response / chromatin binding / chromatin / protein kinase binding / structural molecule activity / mitochondrion / nucleus / cytosol
Similarity search - Function
Sister chromatid cohesion protein Pds5 / non-SMC mitotic condensation complex subunit 1 / Sister chromatid cohesion protein PDS5 protein / 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-like helical ...Sister chromatid cohesion protein Pds5 / non-SMC mitotic condensation complex subunit 1 / Sister chromatid cohesion protein PDS5 protein / 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-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Sister chromatid cohesion protein PDS5 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.073 Å
AuthorsMuir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D.
CitationJournal: Cell Rep. / Year: 2016
Title: Structure of the Pds5-Scc1 Complex and Implications for Cohesin Function
Authors: Muir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D.
History
DepositionDec 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SISTER CHROMATID COHESION PROTEIN PDS5
C: SISTER CHROMATID COHESION PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)82,6292
Polymers82,6292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13.5 kcal/mol
Surface area34270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.471, 248.461, 62.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SISTER CHROMATID COHESION PROTEIN PDS5 / PRECOCIOUS DISSOCIATION OF SISTERS PROTEIN 5 / PDS5


Mass: 80738.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q04264
#2: Protein/peptide SISTER CHROMATID COHESION PROTEIN 1 / SCC1


Mass: 1891.190 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 126-142 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12158

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 29319 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 177.72 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 8.39
Reflection shellMean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.073→48.378 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1024 4.8 %
Rwork0.2188 --
obs0.2204 21226 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92 Å2
Refinement stepCycle: LAST / Resolution: 4.073→48.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5623 0 0 0 5623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065729
X-RAY DIFFRACTIONf_angle_d0.8447771
X-RAY DIFFRACTIONf_dihedral_angle_d13.842137
X-RAY DIFFRACTIONf_chiral_restr0.034914
X-RAY DIFFRACTIONf_plane_restr0.004984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0729-4.28750.3879850.3652061X-RAY DIFFRACTION66
4.2875-4.55590.31461430.2812765X-RAY DIFFRACTION90
4.5559-4.90740.31841380.23983080X-RAY DIFFRACTION100
4.9074-5.40060.28691580.22893066X-RAY DIFFRACTION100
5.4006-6.18070.28521430.22743095X-RAY DIFFRACTION100
6.1807-7.78180.27861820.24823077X-RAY DIFFRACTION100
7.7818-48.3810.20361750.17673058X-RAY DIFFRACTION100

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