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

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Basic information

Entry
Database: PDB / ID: 5hog
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.
Components
  • DNA polymerase alpha-binding protein
  • Dna2p
KeywordsREPLICATION / DNA replication / adaptor protein / beta-propeller domain
Function / homology
Function and homology information


DNA hairpin binding / : / meiotic DNA double-strand break processing / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / single-stranded 3'-5' DNA helicase activity / cohesin loader activity / establishment of sister chromatid cohesion / double-stranded DNA helicase activity ...DNA hairpin binding / : / meiotic DNA double-strand break processing / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / single-stranded 3'-5' DNA helicase activity / cohesin loader activity / establishment of sister chromatid cohesion / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / Cul8-RING ubiquitin ligase complex / Removal of the Flap Intermediate / single-stranded DNA endodeoxyribonuclease activity / 5'-flap endonuclease activity / four-way junction helicase activity / DNA clamp loader activity / nuclease activity / DNA double-strand break processing / replication fork reversal / lagging strand elongation / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / single-stranded DNA helicase activity / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / four-way junction DNA binding / telomere maintenance / DNA helicase activity / protein serine/threonine kinase activator activity / DNA-templated DNA replication / mitotic cell cycle / nucleosome assembly / site of double-strand break / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / DNA helicase / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA repair / DNA damage response / chromatin binding / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / PD-(D/E)XK endonuclease-like domain superfamily / DNA2/NAM7 helicase, helicase domain / AAA domain ...DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / PD-(D/E)XK endonuclease-like domain superfamily / DNA2/NAM7 helicase, helicase domain / AAA domain / : / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA replication ATP-dependent helicase/nuclease DNA2 / DNA polymerase alpha-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.092 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: Dna2p
E: Dna2p


Theoretical massNumber of molelcules
Total (without water)167,1795
Polymers167,1795
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-43 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.677, 99.551, 218.373
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 450-927
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 Dna2p


Mass: 1918.045 Da / Num. of mol.: 2 / Fragment: UNP residues 207-223 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to amino acids 207 to 223 of yeast Dna2.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0D4IHI3, UniProt: P38859*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
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: 0.91915 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91915 Å / Relative weight: 1
ReflectionResolution: 3.09→48.98 Å / Num. obs: 36111 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 9.8
Reflection shellResolution: 3.09→3.23 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 3.092→48.98 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3439 5.05 %Random selection
Rwork0.1802 ---
obs0.1826 68099 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.092→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9503 0 0 71 9574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029775
X-RAY DIFFRACTIONf_angle_d0.50513250
X-RAY DIFFRACTIONf_dihedral_angle_d9.4945842
X-RAY DIFFRACTIONf_chiral_restr0.041428
X-RAY DIFFRACTIONf_plane_restr0.0041704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0916-3.1340.36571190.32412413X-RAY DIFFRACTION93
3.134-3.17870.31421360.29942621X-RAY DIFFRACTION100
3.1787-3.22620.27851260.272598X-RAY DIFFRACTION100
3.2262-3.27660.32871300.28962628X-RAY DIFFRACTION100
3.2766-3.33030.36991380.27582546X-RAY DIFFRACTION100
3.3303-3.38770.28591440.24262607X-RAY DIFFRACTION100
3.3877-3.44930.3181310.22732597X-RAY DIFFRACTION100
3.4493-3.51560.26161470.22592630X-RAY DIFFRACTION100
3.5156-3.58730.29031490.21362542X-RAY DIFFRACTION100
3.5873-3.66530.26041340.2152583X-RAY DIFFRACTION100
3.6653-3.75050.25571320.20692608X-RAY DIFFRACTION100
3.7505-3.84430.2121240.19792622X-RAY DIFFRACTION100
3.8443-3.94820.2251280.19592584X-RAY DIFFRACTION100
3.9482-4.06430.31671430.17282611X-RAY DIFFRACTION100
4.0643-4.19540.1935960.15872647X-RAY DIFFRACTION100
4.1954-4.34530.23021540.14622558X-RAY DIFFRACTION100
4.3453-4.51920.19241520.13862581X-RAY DIFFRACTION100
4.5192-4.72470.14641790.132567X-RAY DIFFRACTION100
4.7247-4.97360.17371530.12712593X-RAY DIFFRACTION100
4.9736-5.28480.16051450.13862556X-RAY DIFFRACTION100
5.2848-5.69230.2171390.15162572X-RAY DIFFRACTION100
5.6923-6.26410.19061320.16352631X-RAY DIFFRACTION100
6.2641-7.16810.21081560.17472556X-RAY DIFFRACTION100
7.1681-9.02180.20171190.15072632X-RAY DIFFRACTION100
9.0218-48.98790.21581330.16862577X-RAY DIFFRACTION99

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