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

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Basic information

Entry
Database: PDB / ID: 5frp
TitleStructure of the Pds5-Scc1 complex and implications for cohesin function
Components
  • MCD1-LIKE PROTEIN
  • SISTER CHROMATID COHESION PROTEIN PDS5
KeywordsCELL CYCLE / CELL DIVISION / 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 / meiotic DNA double-strand break formation / mitotic cohesin complex / cohesin complex / 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 / meiotic DNA double-strand break formation / mitotic cohesin complex / cohesin complex / 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 / OTHER / Resolution: 2.895 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 21, 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 1.3Apr 27, 2016Group: Data collection
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_wavelength_list
Revision 2.1May 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
B: SISTER CHROMATID COHESION PROTEIN PDS5
C: MCD1-LIKE PROTEIN
D: MCD1-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)171,3874
Polymers171,3874
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-31.6 kcal/mol
Surface area63530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.234, 62.562, 155.941
Angle α, β, γ (deg.)90.00, 103.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04264
#2: Protein/peptide MCD1-LIKE PROTEIN


Mass: 4955.659 Da / Num. of mol.: 2
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 / Number of used crystals: 100

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.76 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 59992 / % possible obs: 96.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.58 % / Biso Wilson estimate: 88.35 Å2 / Rmerge(I) obs: 0.5 / Net I/σ(I): 9.14

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.895→48.22 Å / SU ML: 0.53 / σ(F): 0.11 / Phase error: 35.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 5859 5 %
Rwork0.2656 --
obs0.2672 59974 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106 Å2
Refinement stepCycle: LAST / Resolution: 2.895→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 0 0 11116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311322
X-RAY DIFFRACTIONf_angle_d0.6815355
X-RAY DIFFRACTIONf_dihedral_angle_d13.1454211
X-RAY DIFFRACTIONf_chiral_restr0.0411815
X-RAY DIFFRACTIONf_plane_restr0.0041936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8949-2.92780.43181190.38033119X-RAY DIFFRACTION82
2.9278-2.96230.38582000.38583519X-RAY DIFFRACTION91
2.9623-2.99840.43261610.39163487X-RAY DIFFRACTION92
2.9984-3.03630.36061720.38263562X-RAY DIFFRACTION94
3.0363-3.07630.38582010.37123561X-RAY DIFFRACTION94
3.0763-3.11840.39092210.35183685X-RAY DIFFRACTION95
3.1184-3.1630.4452080.34963537X-RAY DIFFRACTION96
3.163-3.21020.4031910.34253712X-RAY DIFFRACTION97
3.2102-3.26030.40011960.34063741X-RAY DIFFRACTION98
3.2603-3.31380.36721880.33953775X-RAY DIFFRACTION99
3.3138-3.37090.37291940.34333708X-RAY DIFFRACTION99
3.3709-3.43220.36041740.32873813X-RAY DIFFRACTION98
3.4322-3.49820.3761910.31433802X-RAY DIFFRACTION98
3.4982-3.56950.34921760.32263736X-RAY DIFFRACTION98
3.5695-3.64710.34961780.31353785X-RAY DIFFRACTION98
3.6471-3.73190.33452110.3113721X-RAY DIFFRACTION98
3.7319-3.82520.36092170.30423676X-RAY DIFFRACTION99
3.8252-3.92860.32612050.28273817X-RAY DIFFRACTION99
3.9286-4.04420.30291720.25923704X-RAY DIFFRACTION99
4.0442-4.17460.2672120.25493832X-RAY DIFFRACTION99
4.1746-4.32370.27112140.24113729X-RAY DIFFRACTION99
4.3237-4.49670.25861830.22863790X-RAY DIFFRACTION99
4.4967-4.70120.28762410.23363672X-RAY DIFFRACTION98
4.7012-4.94890.2751830.24363729X-RAY DIFFRACTION98
4.9489-5.25860.29912430.24893750X-RAY DIFFRACTION99
5.2586-5.6640.28222010.25673805X-RAY DIFFRACTION99
5.664-6.23290.30832260.26123745X-RAY DIFFRACTION99
6.2329-7.13230.2631690.26513744X-RAY DIFFRACTION99
7.1323-8.97650.23852120.2063730X-RAY DIFFRACTION98
8.9765-48.2270.23212000.21263631X-RAY DIFFRACTION96

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