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- PDB-4fvm: Crystal structure of yeast DNA polymerase alpha -

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Basic information

Entry
Database: PDB / ID: 4fvm
TitleCrystal structure of yeast DNA polymerase alpha
ComponentsDNA polymerase alpha catalytic subunit A
KeywordsTRANSFERASE / DNA Polymerase / DNA replication
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / H3-H4 histone complex chaperone activity / DNA replication initiation / RNA-templated DNA biosynthetic process / 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 ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / H3-H4 histone complex chaperone activity / DNA replication initiation / RNA-templated DNA biosynthetic process / 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 / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / DNA replication initiation / replication fork / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / chromatin binding / mitochondrion / zinc ion binding
Similarity search - Function
B family DNA polymerase, thumb domain, alpha/beta motif / B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / Helicase, Ruva Protein; domain 3 / 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 ...B family DNA polymerase, thumb domain, alpha/beta motif / B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / Helicase, Ruva Protein; domain 3 / 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 / Ribonuclease H-like motif / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Helix non-globular / Ribonuclease H-like superfamily/Ribonuclease H / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPerera, R.L. / Pellegrini, L.
CitationJournal: eLife / Year: 2013
Title: Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha
Authors: Perera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / Pellegrini, L.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase alpha catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)103,5321
Polymers103,5321
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.380, 127.140, 74.570
Angle α, β, γ (deg.)90.00, 104.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 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


Mass: 103531.828 Da / Num. of mol.: 1 / Fragment: Polymerase domain, UNP residues 349-1258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC17, N2181, POL1, YNL102W / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: P13382, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 0.1M Bicine, 6% PEG8000, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.3→53.51 Å / Num. all: 58906 / Num. obs: 58906 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 42.31 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3 / Num. unique all: 8523 / Rsym value: 0.512 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1078)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B08

4b08


Resolution: 2.3→36.512 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / Phase error: 30.37 / Stereochemistry target values: ML
Details: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. THE STRUCTURE WAS REFINED WITH RIDING HYDROGENS. THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2970 5.05 %RANDOM
Rwork0.2052 ---
all0.2068 58809 --
obs0.2068 58809 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→36.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6627 0 0 216 6843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026812
X-RAY DIFFRACTIONf_angle_d0.5869222
X-RAY DIFFRACTIONf_dihedral_angle_d12.142630
X-RAY DIFFRACTIONf_chiral_restr0.0371047
X-RAY DIFFRACTIONf_plane_restr0.0021196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33770.37531310.31532648X-RAY DIFFRACTION98
2.3377-2.3780.31471220.30492628X-RAY DIFFRACTION99
2.378-2.42120.32531260.27642671X-RAY DIFFRACTION99
2.4212-2.46780.33391370.2692654X-RAY DIFFRACTION99
2.4678-2.51820.28871180.25662645X-RAY DIFFRACTION98
2.5182-2.57290.28841550.24342667X-RAY DIFFRACTION99
2.5729-2.63270.27031240.23852622X-RAY DIFFRACTION99
2.6327-2.69860.27661520.22652660X-RAY DIFFRACTION99
2.6986-2.77150.30191310.21622665X-RAY DIFFRACTION99
2.7715-2.8530.26431360.20982683X-RAY DIFFRACTION99
2.853-2.94510.25121520.20542667X-RAY DIFFRACTION100
2.9451-3.05030.22951330.21582650X-RAY DIFFRACTION99
3.0503-3.17230.28241610.22542646X-RAY DIFFRACTION99
3.1723-3.31660.24511480.21492685X-RAY DIFFRACTION100
3.3166-3.49140.24891490.21452664X-RAY DIFFRACTION100
3.4914-3.70990.23311310.20182701X-RAY DIFFRACTION99
3.7099-3.9960.23691620.19772660X-RAY DIFFRACTION100
3.996-4.39750.20371500.17692681X-RAY DIFFRACTION100
4.3975-5.03250.1731700.16032678X-RAY DIFFRACTION100
5.0325-6.3350.21831510.19162691X-RAY DIFFRACTION100
6.335-36.51680.2111310.18872573X-RAY DIFFRACTION93

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