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- PDB-4fxd: Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA -

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Basic information

Entry
Database: PDB / ID: 4fxd
TitleCrystal structure of yeast DNA polymerase alpha bound to DNA/RNA
Components
  • DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
  • DNA polymerase alpha catalytic subunit A
  • RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
KeywordsTRANSFERASE/DNA/RNA / DNA polymerase / DNA replication / TRANSFERASE-DNA-RNA complex
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, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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 / 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 / Topoisomerase I; Chain A, domain 4 / 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 / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA polymerase alpha catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPerera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / 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
DepositionJul 3, 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
B: DNA polymerase alpha catalytic subunit A
C: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
E: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')
D: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
F: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)223,2386
Polymers223,2386
Non-polymers00
Water00
1
A: DNA polymerase alpha catalytic subunit A
C: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
E: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)111,6193
Polymers111,6193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-23 kcal/mol
Surface area41170 Å2
MethodPISA
2
B: DNA polymerase alpha catalytic subunit A
D: DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')
F: RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)111,6193
Polymers111,6193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-15 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.140, 74.770, 116.990
Angle α, β, γ (deg.)82.26, 72.57, 82.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase alpha catalytic subunit A


Mass: 103531.828 Da / Num. of mol.: 2 / 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: DNA chain DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)-3')


Mass: 4792.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#3: RNA chain RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*G)-3')


Mass: 3295.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Bicine, 12% PEG3350, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3→58.77 Å / Num. all: 45027 / Num. obs: 45027 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 91.64 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 13.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6546 / Rsym value: 0.921 / % possible all: 97.5

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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 4FVM

4fvm


Resolution: 3→55.526 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.05 / 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
Rfree0.2848 2264 5.03 %Random
Rwork0.2539 ---
obs0.2555 45009 97.79 %-
all-45009 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL.
Refinement stepCycle: LAST / Resolution: 3→55.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13238 672 0 0 13910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314232
X-RAY DIFFRACTIONf_angle_d0.76619395
X-RAY DIFFRACTIONf_dihedral_angle_d13.5455521
X-RAY DIFFRACTIONf_chiral_restr0.0472222
X-RAY DIFFRACTIONf_plane_restr0.0032388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.06520.41681240.36912660X-RAY DIFFRACTION98
3.0652-3.13650.34151270.34562694X-RAY DIFFRACTION97
3.1365-3.2150.38231490.32642641X-RAY DIFFRACTION98
3.215-3.30190.3771410.3222633X-RAY DIFFRACTION97
3.3019-3.3990.32491490.30662695X-RAY DIFFRACTION98
3.399-3.50870.35771510.30362642X-RAY DIFFRACTION98
3.5087-3.63410.36281260.30132694X-RAY DIFFRACTION98
3.6341-3.77960.32581440.30042685X-RAY DIFFRACTION98
3.7796-3.95150.35221480.28242661X-RAY DIFFRACTION98
3.9515-4.15980.30641290.2752693X-RAY DIFFRACTION98
4.1598-4.42030.30411600.2492670X-RAY DIFFRACTION98
4.4203-4.76150.25911570.23012653X-RAY DIFFRACTION98
4.7615-5.24030.22891450.22982676X-RAY DIFFRACTION98
5.2403-5.99780.30151380.242681X-RAY DIFFRACTION98
5.9978-7.55360.24511370.23452702X-RAY DIFFRACTION98
7.5536-55.53590.21631390.19882665X-RAY DIFFRACTION97

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