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- PDB-3oiq: Crystal structure of yeast telomere protein Cdc13 OB1 and the cat... -

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Basic information

Entry
Database: PDB / ID: 3oiq
TitleCrystal structure of yeast telomere protein Cdc13 OB1 and the catalytic subunit of DNA polymerase alpha Pol1
Components
  • Cell division control protein 13
  • DNA polymerase alpha catalytic subunit A
KeywordsPROTEIN BINDING / OB fold / dimer / dimeric complex
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / CST complex / ribonucleoprotein complex localization / RNA-templated DNA biosynthetic process / DNA replication initiation / telomerase inhibitor activity / translation elongation factor binding / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / CST complex / ribonucleoprotein complex localization / RNA-templated DNA biosynthetic process / DNA replication initiation / telomerase inhibitor activity / translation elongation factor binding / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / regulation of telomere maintenance via telomerase / Activation of the pre-replicative complex / nuclear telomere cap complex / single-stranded telomeric DNA binding / lagging strand elongation / G-rich strand telomeric DNA binding / telomere capping / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / telomere maintenance via telomerase / DNA replication initiation / telomere maintenance / replication fork / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell cycle / cell division / nucleotide binding / chromatin binding / mitochondrion / identical protein binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2380 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #800 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 ...Arc Repressor Mutant, subunit A - #2380 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #800 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit A / Cell division control protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSun, J. / Yang, Y. / Wan, K. / Mao, N. / Yu, T.Y. / Lin, Y.C. / DeZwaan, D.C. / Freeman, B.C. / Lin, J.J. / Lue, N.F. / Lei, M.
CitationJournal: Cell Res. / Year: 2011
Title: Structural bases of dimerization of yeast telomere protein Cdc13 and its interaction with the catalytic subunit of DNA polymerase alpha.
Authors: Sun, J. / Yang, Y. / Wan, K. / Mao, N. / Yu, T.Y. / Lin, Y.C. / DeZwaan, D.C. / Freeman, B.C. / Lin, J.J. / Lue, N.F. / Lei, M.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 26, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 13
B: DNA polymerase alpha catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)30,7132
Polymers30,7132
Non-polymers00
Water61334
1
A: Cell division control protein 13
B: DNA polymerase alpha catalytic subunit A

A: Cell division control protein 13
B: DNA polymerase alpha catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)61,4264
Polymers61,4264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5810 Å2
ΔGint-19 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.698, 72.169, 57.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cell division control protein 13


Mass: 26596.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC13, YDL220C / Production host: Escherichia coli (E. coli) / References: UniProt: P32797
#2: Protein/peptide DNA polymerase alpha catalytic subunit A


Mass: 4116.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P13382
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 23% PEG3350, 0.2M Magnisium formate, 0.1M Tris-HCl, 5mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0782
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 22, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 9997 / Num. obs: 9731 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OIP

3oip


Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2725 1000 RANDOM
Rwork0.2267 --
all-9946 -
obs-9689 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 34 1773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00495
X-RAY DIFFRACTIONc_angle_deg1.00164

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