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- PDB-5msm: Structure of the Dcc1-Ctf8-Ctf18C Trimer -

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Basic information

Entry
Database: PDB / ID: 5msm
TitleStructure of the Dcc1-Ctf8-Ctf18C Trimer
Components
  • Chromosome transmission fidelity protein 18
  • Chromosome transmission fidelity protein 8
  • Sister chromatid cohesion protein DCC1
KeywordsCELL CYCLE / winged-helix / DNA repair
Function / homology
Function and homology information


maintenance of mitotic sister chromatid cohesion / telomere tethering at nuclear periphery / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication ...maintenance of mitotic sister chromatid cohesion / telomere tethering at nuclear periphery / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / RFC1-like, AAA+ ATPase lid domain / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Sister chromatid cohesion protein DCC1 / Chromosome transmission fidelity protein 8 / Chromosome transmission fidelity protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWade, B.O. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustFC0010155 United Kingdom
Cancer Research UKFC0010155 United Kingdom
Medical Research Council (United Kingdom)FC0010155 United Kingdom
CitationJournal: EMBO Rep. / Year: 2017
Title: Structural studies of RFC(C)(tf18) reveal a novel chromatin recruitment role for Dcc1.
Authors: Wade, B.O. / Liu, H.W. / Samora, C.P. / Uhlmann, F. / Singleton, M.R.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Sister chromatid cohesion protein DCC1
B: Chromosome transmission fidelity protein 8
C: Chromosome transmission fidelity protein 18
D: Sister chromatid cohesion protein DCC1
E: Chromosome transmission fidelity protein 8
F: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)136,4786
Polymers136,4786
Non-polymers00
Water4,792266
1
A: Sister chromatid cohesion protein DCC1
B: Chromosome transmission fidelity protein 8
C: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)68,2393
Polymers68,2393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-49 kcal/mol
Surface area27650 Å2
MethodPISA
2
D: Sister chromatid cohesion protein DCC1
E: Chromosome transmission fidelity protein 8
F: Chromosome transmission fidelity protein 18


Theoretical massNumber of molelcules
Total (without water)68,2393
Polymers68,2393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-47 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 164.220, 60.640
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sister chromatid cohesion protein DCC1 / Defective in sister chromatid cohesion protein 1


Mass: 44133.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: DCC1, YCL016C, YCL16C / Production host: Escherichia coli (E. coli) / References: UniProt: P25559
#2: Protein Chromosome transmission fidelity protein 8


Mass: 15189.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF8, YHR191C / Production host: Escherichia coli (E. coli) / References: UniProt: P38877
#3: Protein Chromosome transmission fidelity protein 18


Mass: 8915.728 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF18, CHL12, YMR078C, YM9582.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P49956
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris Propane pH 6.3, 0.2M NaBr and 17% PEG 3,350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.29→60.64 Å / Num. obs: 46232 / % possible obs: 90 % / Redundancy: 3 % / Rmerge(I) obs: 0.08522 / Net I/σ(I): 7.15
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4557 / Mean I/σ(I) obs: 1.31 / Num. unique all: 2926 / % possible all: 57

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSN

5msn


Resolution: 2.29→60.64 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.12
RfactorNum. reflection% reflection
Rfree0.2598 2252 4.87 %
Rwork0.2 --
obs0.2029 46207 89.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.29→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8518 0 0 266 8784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018700
X-RAY DIFFRACTIONf_angle_d1.53111738
X-RAY DIFFRACTIONf_dihedral_angle_d15.6283302
X-RAY DIFFRACTIONf_chiral_restr0.0621308
X-RAY DIFFRACTIONf_plane_restr0.0071484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2902-2.340.34751210.31231687X-RAY DIFFRACTION56
2.34-2.39440.4319880.27951857X-RAY DIFFRACTION61
2.3944-2.45430.40741180.28962174X-RAY DIFFRACTION71
2.4543-2.52060.31191070.2792449X-RAY DIFFRACTION80
2.5206-2.59480.33291430.27342758X-RAY DIFFRACTION91
2.5948-2.67860.31641310.25733075X-RAY DIFFRACTION99
2.6786-2.77430.36731530.25013047X-RAY DIFFRACTION100
2.7743-2.88540.32521490.23463058X-RAY DIFFRACTION100
2.8854-3.01670.2891820.22953028X-RAY DIFFRACTION100
3.0167-3.17580.29171120.22153069X-RAY DIFFRACTION100
3.1758-3.37470.2411370.20613046X-RAY DIFFRACTION99
3.3747-3.63530.24291990.19862966X-RAY DIFFRACTION98
3.6353-4.00110.24341510.17682966X-RAY DIFFRACTION97
4.0011-4.58010.23041620.15632888X-RAY DIFFRACTION95
4.5801-5.77020.22831610.16942888X-RAY DIFFRACTION94
5.7702-82.16280.21041380.17482999X-RAY DIFFRACTION96

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