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- PDB-5hoi: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -

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Basic information

Entry
Database: PDB / ID: 5hoi
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2.
Components
  • DNA polymerase alpha-binding protein
  • Topoisomerase 1-associated factor 2
KeywordsREPLICATION / DNA replication / adaptor protein / beta-propeller domain
Function / homology
Function and homology information


establishment of sister chromatid cohesion / protein localization to nucleolar rDNA repeats / Cul8-RING ubiquitin ligase complex / rDNA chromatin condensation / phosphatase activator activity / rDNA binding / rDNA heterochromatin formation / double-strand break repair via break-induced replication / nucleolus organization / mitotic sister chromatid cohesion ...establishment of sister chromatid cohesion / protein localization to nucleolar rDNA repeats / Cul8-RING ubiquitin ligase complex / rDNA chromatin condensation / phosphatase activator activity / rDNA binding / rDNA heterochromatin formation / double-strand break repair via break-induced replication / nucleolus organization / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / mitotic cell cycle / nucleosome assembly / DNA repair / chromatin binding / nucleolus / mitochondrion / identical protein binding / nucleus
Similarity search - Function
Nucleolar protein Dnt1-like, N-terminal / Dnt1/Tof2/Net1 / Cdc14 phosphatase binding protein N-terminus / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA polymerase alpha-binding protein / Topoisomerase 1-associated factor 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsSimon, A.C. / Pellegrini, L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
Gates Cambridge PhD program United Kingdom
Citation
Journal: Mol.Cell / Year: 2016
Title: Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase.
Authors: Villa, F. / Simon, A.C. / Ortiz Bazan, M.A. / Kilkenny, M.L. / Wirthensohn, D. / Wightman, M. / Matak-Vinkovic, D. / Pellegrini, L. / Labib, K.
#1: Journal: Nature / Year: 2014
Title: A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome.
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / van Deursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
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

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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: Topoisomerase 1-associated factor 2
E: Topoisomerase 1-associated factor 2
F: Topoisomerase 1-associated factor 2


Theoretical massNumber of molelcules
Total (without water)170,8936
Polymers170,8936
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-50 kcal/mol
Surface area50830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.576, 99.546, 218.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein DNA polymerase alpha-binding protein / Chromosome replication protein CHL15 / Chromosome transmission fidelity protein 4 / Protein POB1


Mass: 54447.484 Da / Num. of mol.: 3 / Fragment: UNP residues 472-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTF4, CHL15, POB1, YPR135W, P9659.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01454
#2: Protein/peptide Topoisomerase 1-associated factor 2


Mass: 2516.958 Da / Num. of mol.: 3 / Fragment: UNP residues 497-517 / Source method: obtained synthetically
Details: The synthetic peptide corresponds to amino acids 497 to 517 of yeast Tof2.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.3→48.99 Å / Num. obs: 29749 / % possible obs: 99.3 % / Redundancy: 4.6 % / Net I/σ(I): 8.2
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 3.3→48.99 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2770 4.95 %Random selection
Rwork0.1789 ---
obs0.1812 55965 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 0 51 9615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029847
X-RAY DIFFRACTIONf_angle_d0.45113340
X-RAY DIFFRACTIONf_dihedral_angle_d7.5885899
X-RAY DIFFRACTIONf_chiral_restr0.0391439
X-RAY DIFFRACTIONf_plane_restr0.0031711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2973-3.35410.3621090.31122624X-RAY DIFFRACTION97
3.3541-3.41510.31511460.26482698X-RAY DIFFRACTION100
3.4151-3.48070.28621420.25252598X-RAY DIFFRACTION99
3.4807-3.55180.27421390.24522700X-RAY DIFFRACTION99
3.5518-3.6290.31621280.24452677X-RAY DIFFRACTION100
3.629-3.71340.29021340.23012668X-RAY DIFFRACTION99
3.7134-3.80620.29281610.20752644X-RAY DIFFRACTION100
3.8062-3.90910.27861050.19942679X-RAY DIFFRACTION99
3.9091-4.0240.23751370.18772674X-RAY DIFFRACTION100
4.024-4.15390.21941210.17872671X-RAY DIFFRACTION99
4.1539-4.30220.23051390.17072649X-RAY DIFFRACTION100
4.3022-4.47440.20481490.15292657X-RAY DIFFRACTION99
4.4744-4.67790.19451500.13462620X-RAY DIFFRACTION99
4.6779-4.92430.17881570.13322691X-RAY DIFFRACTION100
4.9243-5.23250.18311450.1422653X-RAY DIFFRACTION100
5.2325-5.63590.19791510.14862623X-RAY DIFFRACTION99
5.6359-6.20210.25711360.1722677X-RAY DIFFRACTION100
6.2021-7.09720.2271320.17522690X-RAY DIFFRACTION100
7.0972-8.93290.17331460.16112661X-RAY DIFFRACTION100
8.9329-48.99740.17841430.16612641X-RAY DIFFRACTION99

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