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- PDB-5me3: Structure of the Scc2 C-terminus -

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Basic information

Entry
Database: PDB / ID: 5me3
TitleStructure of the Scc2 C-terminus
Components
  • (Scc2 unassigned sequence) x 2
  • Sister chromatid cohesion protein 2
  • unassigned sequence of Scc2
KeywordsCELL CYCLE / cohesin loader / HEAT repeat / Scc2
Function / homology
Function and homology information


Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / cohesin loader activity / tRNA gene clustering / rDNA chromatin condensation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / establishment of protein localization to chromatin / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion ...Scc2-Scc4 cohesin loading complex / 2-micrometer circle DNA / cohesin loader activity / tRNA gene clustering / rDNA chromatin condensation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / establishment of protein localization to chromatin / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / chromatin looping / regulation of gene expression / sequence-specific DNA binding / chromatin binding / chromatin / cytosol
Similarity search - Function
HEAT repeat associated with sister chromatid cohesion protein / Sister chromatid cohesion C-terminal domain / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Armadillo-type fold
Similarity search - Domain/homology
Sister chromatid cohesion protein 2
Similarity search - Component
Biological speciesAshbya gossypii (fungus)
Eremothecium gossypii ATCC 10895 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.85 Å
AuthorsChao, W.C.H. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Structure of the cohesin loader Scc2.
Authors: Chao, W.C. / Murayama, Y. / Munoz, S. / Jones, A.W. / Wade, B.O. / Purkiss, A.G. / Hu, X.W. / Borg, A. / Snijders, A.P. / Uhlmann, F. / Singleton, M.R.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Sister chromatid cohesion protein 2
B: Sister chromatid cohesion protein 2
X: unassigned sequence of Scc2
Y: Scc2 unassigned sequence
Z: Scc2 unassigned sequence
W: Scc2 unassigned sequence


Theoretical massNumber of molelcules
Total (without water)268,8116
Polymers268,8116
Non-polymers00
Water00
1
A: Sister chromatid cohesion protein 2
X: unassigned sequence of Scc2
Z: Scc2 unassigned sequence


Theoretical massNumber of molelcules
Total (without water)133,9803
Polymers133,9803
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sister chromatid cohesion protein 2
Y: Scc2 unassigned sequence
W: Scc2 unassigned sequence


Theoretical massNumber of molelcules
Total (without water)134,8313
Polymers134,8313
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.049, 106.440, 143.183
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sister chromatid cohesion protein 2


Mass: 131560.844 Da / Num. of mol.: 2 / Fragment: UNP residues 378-1479
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)
Gene: SCC2, AGL133W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q750S2
#2: Protein/peptide unassigned sequence of Scc2


Mass: 1464.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: unassigned sequence of Scc2
Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus)
Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein/peptide Scc2 unassigned sequence


Mass: 2315.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Scc2 unassigned sequence
Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus)
Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein/peptide Scc2 unassigned sequence


Mass: 954.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus)
Production host: Spodoptera frugiperda (fall armyworm)

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM imidazole (pH 6.8), 200 mM lithium sulphate, and 4.5% polyethylene glycol 5000 MME

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→48.81 Å / Num. obs: 65853 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.0715 / Net I/σ(I): 10.36
Reflection shellResolution: 2.85→2.952 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 0.75 / CC1/2: 0.312 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.85→48.81 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 3385 5.14 %
Rwork0.2175 --
obs0.2201 65846 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16017 0 0 0 16017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416294
X-RAY DIFFRACTIONf_angle_d0.86222009
X-RAY DIFFRACTIONf_dihedral_angle_d15.8339931
X-RAY DIFFRACTIONf_chiral_restr0.0462579
X-RAY DIFFRACTIONf_plane_restr0.0052747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.89070.41591260.36232429X-RAY DIFFRACTION92
2.8907-2.93390.44561500.37262557X-RAY DIFFRACTION99
2.9339-2.97970.41081290.34952668X-RAY DIFFRACTION100
2.9797-3.02860.36791540.34382570X-RAY DIFFRACTION100
3.0286-3.08080.37341580.32522635X-RAY DIFFRACTION100
3.0808-3.13680.33331310.31022595X-RAY DIFFRACTION100
3.1368-3.19710.40011300.30972654X-RAY DIFFRACTION100
3.1971-3.26240.34661400.292611X-RAY DIFFRACTION100
3.2624-3.33330.36391250.28582630X-RAY DIFFRACTION100
3.3333-3.41080.30521390.26462613X-RAY DIFFRACTION100
3.4108-3.49610.30591440.26492664X-RAY DIFFRACTION100
3.4961-3.59060.31691410.25682586X-RAY DIFFRACTION100
3.5906-3.69620.28521540.21442614X-RAY DIFFRACTION100
3.6962-3.81550.24491100.19592657X-RAY DIFFRACTION100
3.8155-3.95180.24461530.1962616X-RAY DIFFRACTION99
3.9518-4.10990.23261670.19832609X-RAY DIFFRACTION99
4.1099-4.29690.26781640.18922565X-RAY DIFFRACTION99
4.2969-4.52330.22981690.17872589X-RAY DIFFRACTION99
4.5233-4.80650.23351290.17872608X-RAY DIFFRACTION98
4.8065-5.17720.24211250.18462619X-RAY DIFFRACTION98
5.1772-5.69750.2471330.21612573X-RAY DIFFRACTION97
5.6975-6.52040.29031600.24622577X-RAY DIFFRACTION97
6.5204-8.2090.23351290.2052597X-RAY DIFFRACTION97
8.209-49.69120.23431250.18242625X-RAY DIFFRACTION96

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