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- PDB-5w94: Crystal structure of Scc4 in complex with Scc2n and Ctf19n -

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Basic information

Entry
Database: PDB / ID: 5w94
TitleCrystal structure of Scc4 in complex with Scc2n and Ctf19n
Components
  • Ctf19n
  • MAU2 chromatid cohesion factor homolog
  • Sister chromatid cohesion protein 2
KeywordsCELL CYCLE / Cohesin / kinetochore / centromere
Function / homology
Function and homology information


SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / COMA complex / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of spindle microtubules to kinetochore ...SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / COMA complex / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of spindle microtubules to kinetochore / kinetochore binding / replication-born double-strand break repair via sister chromatid exchange / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / chromosome, centromeric region / protein localization to chromatin / meiotic cell cycle / chromosome segregation / kinetochore / double-strand break repair / regulation of gene expression / sequence-specific DNA binding / cell division / chromatin binding / chromatin / nucleus / cytosol
Similarity search - Function
Chromatid cohesion factor MAU2 / Cohesin loading factor / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Putative AMP-binding domain signature. / Armadillo-type fold
Similarity search - Domain/homology
MAU2 chromatid cohesion factor homolog / Inner kinetochore subunit CTF19 / Sister chromatid cohesion protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.193 Å
AuthorsHinshaw, S.M. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2017
Title: The Kinetochore Receptor for the Cohesin Loading Complex.
Authors: Hinshaw, S.M. / Makrantoni, V. / Harrison, S.C. / Marston, A.L.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAU2 chromatid cohesion factor homolog
B: Sister chromatid cohesion protein 2
C: MAU2 chromatid cohesion factor homolog
D: Sister chromatid cohesion protein 2
E: Ctf19n
H: Ctf19n


Theoretical massNumber of molelcules
Total (without water)185,8236
Polymers185,8236
Non-polymers00
Water0
1
A: MAU2 chromatid cohesion factor homolog
B: Sister chromatid cohesion protein 2
E: Ctf19n


Theoretical massNumber of molelcules
Total (without water)92,9113
Polymers92,9113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-91 kcal/mol
Surface area32910 Å2
MethodPISA
2
C: MAU2 chromatid cohesion factor homolog
D: Sister chromatid cohesion protein 2
H: Ctf19n


Theoretical massNumber of molelcules
Total (without water)92,9113
Polymers92,9113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-89 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.969, 172.969, 145.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein MAU2 chromatid cohesion factor homolog / Sister chromatid cohesion protein 4


Mass: 72226.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCC4, YER147C / Production host: Escherichia coli (E. coli) / References: UniProt: P40090
#2: Protein Sister chromatid cohesion protein 2


Mass: 19810.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCC2, YDR180W, YD9395.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04002
#3: Protein/peptide Ctf19n


Mass: 874.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02732*PLUS

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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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 6 / Details: 8% PEG4000, 80 mM PIPES, pH 6.0

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Data collection

DiffractionMean temperature: 63 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 28, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.19→39.94 Å / Num. obs: 40688 / % possible obs: 99.11 % / Redundancy: 10.6 % / Rsym value: 0.055 / Net I/σ(I): 24.37
Reflection shellHighest resolution: 3.19 Å / Rsym value: 1.06

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XDN

4xdn


Resolution: 3.193→39.94 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.62
RfactorNum. reflection% reflection
Rfree0.2579 1996 4.91 %
Rwork0.2088 --
obs0.2112 40629 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.193→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11738 0 0 0 11738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111962
X-RAY DIFFRACTIONf_angle_d1.41616142
X-RAY DIFFRACTIONf_dihedral_angle_d16.9574490
X-RAY DIFFRACTIONf_chiral_restr0.0691813
X-RAY DIFFRACTIONf_plane_restr0.0082030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1927-3.27250.43411260.38172476X-RAY DIFFRACTION88
3.2725-3.36090.39091440.34312747X-RAY DIFFRACTION100
3.3609-3.45980.40191480.32442791X-RAY DIFFRACTION100
3.4598-3.57140.351390.30252746X-RAY DIFFRACTION100
3.5714-3.69890.34911450.30372790X-RAY DIFFRACTION100
3.6989-3.84690.32351410.26122764X-RAY DIFFRACTION100
3.8469-4.02180.29031410.23572792X-RAY DIFFRACTION100
4.0218-4.23370.26541440.20762756X-RAY DIFFRACTION100
4.2337-4.49860.23761480.19532764X-RAY DIFFRACTION100
4.4986-4.84540.26751400.17662801X-RAY DIFFRACTION100
4.8454-5.3320.23141410.17822769X-RAY DIFFRACTION100
5.332-6.10120.24711430.19392807X-RAY DIFFRACTION100
6.1012-7.67790.25341450.21612802X-RAY DIFFRACTION100
7.6779-39.94380.19331510.15492828X-RAY DIFFRACTION100

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