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- PDB-4c95: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -

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Basic information

Entry
Database: PDB / ID: 4c95
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Sld5
Components
  • DNA POLYMERASE ALPHA-BINDING PROTEIN
  • DNA REPLICATION COMPLEX GINS PROTEIN SLD5
KeywordsDNA REPLICATION / ADAPTOR PROTEIN / BETA PROPELLER DOMAIN
Function / homology
Function and homology information


establishment of sister chromatid cohesion / Unwinding of DNA / Cul8-RING ubiquitin ligase complex / GINS complex / CMG complex / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome ...establishment of sister chromatid cohesion / Unwinding of DNA / Cul8-RING ubiquitin ligase complex / GINS complex / CMG complex / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly / mitotic cell cycle / DNA repair / chromatin binding / identical protein binding / nucleus
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A ...: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA polymerase alpha-binding protein / DNA replication complex GINS protein SLD5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.694 Å
AuthorsSimon, A.C. / Pellegrini, L.
CitationJournal: Nature / Year: 2014
Title: A Ctf4 Trimer Couples the Cmg Helicase to DNA Polymerase a in the Eukaryotic Replisome
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / Vandeursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE ALPHA-BINDING PROTEIN
B: DNA POLYMERASE ALPHA-BINDING PROTEIN
C: DNA POLYMERASE ALPHA-BINDING PROTEIN
D: DNA REPLICATION COMPLEX GINS PROTEIN SLD5
E: DNA REPLICATION COMPLEX GINS PROTEIN SLD5


Theoretical massNumber of molelcules
Total (without water)167,5835
Polymers167,5835
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-46.3 kcal/mol
Surface area50010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.944, 99.705, 218.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-2008-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein DNA POLYMERASE ALPHA-BINDING PROTEIN / CHROMOSOME REPLICATION PROTEIN CHL15 / CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 / PROTEIN POB1 / CTF4


Mass: 54447.484 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 471-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q01454
#2: Protein/peptide DNA REPLICATION COMPLEX GINS PROTEIN SLD5 / SLD5


Mass: 2120.355 Da / Num. of mol.: 2 / Fragment: CTF4-BINDING MOTIF, RESIDUES 1-19 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q03406
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3 Å3/Da / Density % sol: 59.1 % / Description: NONE
Crystal growDetails: 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.69→49.07 Å / Num. obs: 54280 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.3
Reflection shellResolution: 2.69→2.77 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.694→47.919 Å / SU ML: 0.33 / σ(F): 0.19 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 5263 5.1 %
Rwork0.1787 --
obs0.1805 54188 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.694→47.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9477 0 0 183 9660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029749
X-RAY DIFFRACTIONf_angle_d0.62913217
X-RAY DIFFRACTIONf_dihedral_angle_d11.3173597
X-RAY DIFFRACTIONf_chiral_restr0.0271426
X-RAY DIFFRACTIONf_plane_restr0.0031699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6943-2.72490.32611300.31472608X-RAY DIFFRACTION80
2.7249-2.75690.31431770.29953292X-RAY DIFFRACTION100
2.7569-2.79060.3412190.29373268X-RAY DIFFRACTION100
2.7906-2.82590.30592070.28313207X-RAY DIFFRACTION100
2.8259-2.86310.31871970.27513265X-RAY DIFFRACTION100
2.8631-2.90230.321280.26653345X-RAY DIFFRACTION100
2.9023-2.94370.34511890.26893249X-RAY DIFFRACTION100
2.9437-2.98770.30441790.25243259X-RAY DIFFRACTION100
2.9877-3.03430.29851580.24273341X-RAY DIFFRACTION100
3.0343-3.08410.24961610.23583311X-RAY DIFFRACTION100
3.0841-3.13730.25271700.22333271X-RAY DIFFRACTION100
3.1373-3.19430.27571810.21363287X-RAY DIFFRACTION100
3.1943-3.25570.27541840.20753269X-RAY DIFFRACTION100
3.2557-3.32220.23591890.20343292X-RAY DIFFRACTION100
3.3222-3.39440.22541850.19413224X-RAY DIFFRACTION100
3.3944-3.47330.25651620.18353294X-RAY DIFFRACTION100
3.4733-3.56010.24941750.18523358X-RAY DIFFRACTION100
3.5601-3.65640.25151530.16823228X-RAY DIFFRACTION100
3.6564-3.76390.22641740.16493296X-RAY DIFFRACTION100
3.7639-3.88540.18621670.15693291X-RAY DIFFRACTION100
3.8854-4.02420.16852100.1583248X-RAY DIFFRACTION100
4.0242-4.18520.17291710.14853291X-RAY DIFFRACTION100
4.1852-4.37550.15321550.14143305X-RAY DIFFRACTION100
4.3755-4.60610.1761650.14133304X-RAY DIFFRACTION100
4.6061-4.89440.15481910.13513259X-RAY DIFFRACTION100
4.8944-5.27180.19031600.14663294X-RAY DIFFRACTION100
5.2718-5.80160.20171830.15363300X-RAY DIFFRACTION100
5.8016-6.63920.19741670.16873298X-RAY DIFFRACTION100
6.6392-8.35740.1871820.16793272X-RAY DIFFRACTION100
8.3574-47.92690.18561940.15963246X-RAY DIFFRACTION100

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