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- PDB-4xdn: Crystal structure of Scc4 in complex with Scc2n -

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Basic information

Entry
Database: PDB / ID: 4xdn
TitleCrystal structure of Scc4 in complex with Scc2n
Components
  • MAU2 chromatid cohesion factor homolog
  • Sister chromatid cohesion protein 2
KeywordsCELL CYCLE / cohesion / centromere / cohesin loading
Function / homology
Function and homology information


SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / replication-born double-strand break repair via sister chromatid exchange ...SMC loading complex / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / mitotic sister chromatid cohesion / chromosome, centromeric region / protein localization to chromatin / 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 / Sister chromatid cohesion protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsHinshaw, S.M. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2015
Title: Structural evidence for Scc4-dependent localization of cohesin loading.
Authors: Hinshaw, S.M. / Makrantoni, V. / Kerr, A. / Marston, A.L. / Harrison, S.C.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9067
Polymers96,4262
Non-polymers4805
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-163 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.579, 177.279, 51.343
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 74557.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCC4 / Production host: Escherichia coli (E. coli) / References: UniProt: P40090
#2: Protein Sister chromatid cohesion protein 2


Mass: 21868.424 Da / Num. of mol.: 1 / Fragment: N-terminal region (UNP residues 1-181)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04002
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: overnight growth in .2M ammonium sulfate, 16% (w:v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.079→30 Å / Num. obs: 50794 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 2.079→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.762 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SHELXDEphasing
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.08→28.72 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1866 3.95 %Random selection
Rwork0.185 ---
obs0.186 47188 91.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.5 Å2
Refinement stepCycle: LAST / Resolution: 2.08→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 25 301 6189

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