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- PDB-5c6g: Structural Insights into the Scc2-Scc4 Cohesin Loader -

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Basic information

Entry
Database: PDB / ID: 5c6g
TitleStructural Insights into the Scc2-Scc4 Cohesin Loader
Components
  • AGR133Cp
  • Sister chromatid cohesion protein 2
KeywordsCELL CYCLE / cohesin loader / TPR repeat
Function / homology
Function and homology information


SMC loading complex / positive regulation of mitotic cohesin loading / Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / tRNA gene clustering / rDNA condensation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / establishment of protein localization to chromatin / kinetochore binding / establishment of mitotic sister chromatid cohesion ...SMC loading complex / positive regulation of mitotic cohesin loading / Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / tRNA gene clustering / rDNA condensation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / establishment of protein localization to chromatin / kinetochore binding / establishment of mitotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / chromatin => GO:0000785 / mitotic chromosome condensation / mitotic sister chromatid cohesion / double-strand break repair / regulation of gene expression / sequence-specific DNA binding / chromatin / chromatin binding / cytosol
Similarity search - Function
Cohesin loading factor / Chromatid cohesion factor MAU2 / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / HEAT repeat associated with sister chromatid cohesion / Armadillo-type fold
Similarity search - Domain/homology
AGR133Cp / Sister chromatid cohesion protein 2
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSingleton, M.R. / Chao, W.C.H.
CitationJournal: Cell Rep / Year: 2015
Title: Structural Studies Reveal the Functional Modularity of the Scc2-Scc4 Cohesin Loader.
Authors: Chao, W.C. / Murayama, Y. / Munoz, S. / Costa, A. / Uhlmann, F. / Singleton, M.R.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGR133Cp
B: Sister chromatid cohesion protein 2
C: AGR133Cp
D: Sister chromatid cohesion protein 2


Theoretical massNumber of molelcules
Total (without water)190,3244
Polymers190,3244
Non-polymers00
Water18010
1
A: AGR133Cp
B: Sister chromatid cohesion protein 2


Theoretical massNumber of molelcules
Total (without water)95,1622
Polymers95,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-81 kcal/mol
Surface area32430 Å2
MethodPISA
2
C: AGR133Cp
D: Sister chromatid cohesion protein 2


Theoretical massNumber of molelcules
Total (without water)95,1622
Polymers95,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-73 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)112.240, 88.810, 116.000
Angle α, β, γ (deg.)90.00, 118.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AGR133Cp


Mass: 70537.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 34-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (fungus) / Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AGR133C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q74ZR5
#2: Protein Sister chromatid cohesion protein 2


Mass: 24624.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus)
Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: SCC2, AGL133W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q750S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, cacodylate. calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.55→98.66 Å / Num. obs: 63440 / % possible obs: 96.76 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.96
Reflection shellResolution: 2.55→2.62 Å / Rmerge(I) obs: 0.591

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→98.648 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2743 2991 5 %
Rwork0.2274 --
obs0.2297 59831 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→98.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11553 0 0 10 11563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911753
X-RAY DIFFRACTIONf_angle_d1.23115902
X-RAY DIFFRACTIONf_dihedral_angle_d19.8314389
X-RAY DIFFRACTIONf_chiral_restr0.0471848
X-RAY DIFFRACTIONf_plane_restr0.0042015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64260.36641550.30352701X-RAY DIFFRACTION98
2.6426-2.68820.31431370.30222734X-RAY DIFFRACTION98
2.6882-2.73710.33271560.29662689X-RAY DIFFRACTION98
2.7371-2.78970.37231480.30852726X-RAY DIFFRACTION98
2.7897-2.84670.34961300.30222755X-RAY DIFFRACTION98
2.8467-2.90860.33291310.30042753X-RAY DIFFRACTION98
2.9086-2.97630.33251430.28862713X-RAY DIFFRACTION98
2.9763-3.05070.35041430.29342757X-RAY DIFFRACTION98
3.0507-3.13320.30091330.28722662X-RAY DIFFRACTION96
3.1332-3.22540.38661270.28112702X-RAY DIFFRACTION96
3.2254-3.32950.29421590.27122738X-RAY DIFFRACTION99
3.3295-3.44850.31351340.26452736X-RAY DIFFRACTION98
3.4485-3.58660.28321250.25362767X-RAY DIFFRACTION98
3.5866-3.74980.28831670.23962703X-RAY DIFFRACTION98
3.7498-3.94750.27821600.2342674X-RAY DIFFRACTION97
3.9475-4.19480.25431520.2162712X-RAY DIFFRACTION97
4.1948-4.51870.24431370.2122636X-RAY DIFFRACTION94
4.5187-4.97350.23251500.20262605X-RAY DIFFRACTION93
4.9735-5.69310.27531320.20842703X-RAY DIFFRACTION95
5.6931-7.17240.3021580.21072665X-RAY DIFFRACTION94
7.1724-98.71880.18851140.16242709X-RAY DIFFRACTION92

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