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- PDB-4c93: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -

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Basic information

Entry
Database: PDB / ID: 4c93
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha.
Components
  • DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A
  • DNA POLYMERASE ALPHA-BINDING PROTEIN
KeywordsDNA REPLICATION / ADAPTOR PROTEIN / BETA PROPELLER DOMAIN
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation / replication fork protection complex / mitotic DNA replication initiation / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / DNA synthesis involved in DNA repair / leading strand elongation / nuclear replication fork / DNA replication origin binding / DNA replication initiation / replication fork / DNA-templated DNA replication / double-strand break repair / nucleosome assembly / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / mitochondrion / identical protein binding / nucleus / metal ion binding
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 polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain ...: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit A / DNA polymerase alpha-binding protein
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 POLYMERASE ALPHA CATALYTIC SUBUNIT A
E: DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)166,3705
Polymers166,3705
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-38.7 kcal/mol
Surface area49690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.977, 99.998, 219.546
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-2010-

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 POLYMERASE ALPHA CATALYTIC SUBUNIT A / DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\: PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE- ...DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\: PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE-PRIMASE COMPLEX P180 SUBUNIT / POL ALPHA-PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE ALPHA CATALYTIC SUBUNIT


Mass: 1513.560 Da / Num. of mol.: 2 / Fragment: CTF4-BINDING MOTIF, RESIDUES 137-149 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P13382, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.03 Å3/Da / Density % sol: 59.4 % / 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: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.69→49.2 Å / Num. obs: 54802 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 53.35 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.2
Reflection shellResolution: 2.69→2.77 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.4 / % possible all: 95

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Processing

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

Resolution: 2.694→49.205 Å / SU ML: 0.35 / σ(F): 0.08 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 5266 5.1 %
Rwork0.1718 --
obs0.1737 54707 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.2 Å2
Refinement stepCycle: LAST / Resolution: 2.694→49.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9433 0 0 160 9593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039709
X-RAY DIFFRACTIONf_angle_d0.66713161
X-RAY DIFFRACTIONf_dihedral_angle_d11.9573573
X-RAY DIFFRACTIONf_chiral_restr0.0281412
X-RAY DIFFRACTIONf_plane_restr0.0041693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6942-2.72490.34541560.35412811X-RAY DIFFRACTION85
2.7249-2.75690.38021710.32143277X-RAY DIFFRACTION100
2.7569-2.79050.36321520.31033386X-RAY DIFFRACTION100
2.7905-2.82590.29982140.28573224X-RAY DIFFRACTION100
2.8259-2.8630.32922100.27143281X-RAY DIFFRACTION100
2.863-2.90230.28661320.25573360X-RAY DIFFRACTION100
2.9023-2.94370.27451820.24963320X-RAY DIFFRACTION100
2.9437-2.98760.28961800.24463299X-RAY DIFFRACTION100
2.9876-3.03430.29391640.23683328X-RAY DIFFRACTION100
3.0343-3.08410.26571650.23973314X-RAY DIFFRACTION100
3.0841-3.13720.27891760.21743317X-RAY DIFFRACTION100
3.1372-3.19430.2971700.2173314X-RAY DIFFRACTION100
3.1943-3.25570.26471810.20633300X-RAY DIFFRACTION100
3.2557-3.32210.25561920.19743288X-RAY DIFFRACTION100
3.3221-3.39440.23911890.18723293X-RAY DIFFRACTION100
3.3944-3.47330.22581570.16913337X-RAY DIFFRACTION100
3.4733-3.56010.21521890.16533317X-RAY DIFFRACTION100
3.5601-3.65640.22761420.16073318X-RAY DIFFRACTION100
3.6564-3.76390.19271900.16163287X-RAY DIFFRACTION100
3.7639-3.88540.19561650.14273321X-RAY DIFFRACTION100
3.8854-4.02420.18211980.14833321X-RAY DIFFRACTION100
4.0242-4.18520.16511830.13973309X-RAY DIFFRACTION100
4.1852-4.37560.13991590.12943302X-RAY DIFFRACTION100
4.3756-4.60610.17891620.12323327X-RAY DIFFRACTION100
4.6061-4.89440.14621960.12513278X-RAY DIFFRACTION100
4.8944-5.27190.1761620.1343351X-RAY DIFFRACTION100
5.2719-5.80170.1871690.13973315X-RAY DIFFRACTION100
5.8017-6.63950.18711790.1613308X-RAY DIFFRACTION100
6.6395-8.35840.17981810.1553299X-RAY DIFFRACTION100
8.3584-49.21280.1812000.15793273X-RAY DIFFRACTION99

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