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

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Basic information

Entry
Database: PDB / ID: 4fyd
TitleCrystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
Components
  • DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
  • DNA polymerase alpha catalytic subunit A
  • DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA replication / TRANSFERASE-DNA 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
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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-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 / Ribonuclease H-like superfamily/Ribonuclease H / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA polymerase alpha catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionJul 4, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
D: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
E: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
F: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,9328
Polymers229,9186
Non-polymers1,0142
Water00
1
A: DNA polymerase alpha catalytic subunit A
C: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
E: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4664
Polymers114,9593
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-26 kcal/mol
Surface area40620 Å2
MethodPISA
2
B: DNA polymerase alpha catalytic subunit A
D: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
F: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4664
Polymers114,9593
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.689, 145.686, 197.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase alpha catalytic subunit A


Mass: 103401.703 Da / Num. of mol.: 2 / Fragment: Polymerase domain, UNP residues 349-1258 / Mutation: R508A, N509A, D998N
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*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')


Mass: 7627.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#3: DNA/RNA hybrid DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')


Mass: 3929.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3

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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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→49.39 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 97.34 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.8
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8380 / Rsym value: 0.974 / % possible all: 98.4

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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: 3.1→48.801 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.08 / 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
Rfree0.2467 5699 5.08 %Random
Rwork0.2098 ---
obs0.2116 59154 99.21 %-
all-59154 --
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13530 1152 62 0 14744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315128
X-RAY DIFFRACTIONf_angle_d0.65220714
X-RAY DIFFRACTIONf_dihedral_angle_d15.435910
X-RAY DIFFRACTIONf_chiral_restr0.0392364
X-RAY DIFFRACTIONf_plane_restr0.0032464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13220.40811990.38493358X-RAY DIFFRACTION95
3.1322-3.1690.40151850.35883561X-RAY DIFFRACTION99
3.169-3.20770.3711830.33353576X-RAY DIFFRACTION100
3.2077-3.24830.34722210.3253504X-RAY DIFFRACTION99
3.2483-3.2910.30741960.30473587X-RAY DIFFRACTION100
3.291-3.33610.33051800.29193519X-RAY DIFFRACTION99
3.3361-3.38370.33731870.27363635X-RAY DIFFRACTION99
3.3837-3.43420.32371690.27763491X-RAY DIFFRACTION100
3.4342-3.48790.27961780.26383604X-RAY DIFFRACTION99
3.4879-3.5450.34662340.25083556X-RAY DIFFRACTION99
3.545-3.60610.29151680.24933571X-RAY DIFFRACTION100
3.6061-3.67170.26942160.2283502X-RAY DIFFRACTION99
3.6717-3.74230.25652050.2323565X-RAY DIFFRACTION99
3.7423-3.81870.30092000.23923534X-RAY DIFFRACTION99
3.8187-3.90170.35171610.22333602X-RAY DIFFRACTION99
3.9017-3.99240.26051790.21223553X-RAY DIFFRACTION99
3.9924-4.09220.2551910.20663586X-RAY DIFFRACTION100
4.0922-4.20280.24692040.19753539X-RAY DIFFRACTION99
4.2028-4.32630.2651960.18843514X-RAY DIFFRACTION99
4.3263-4.46590.20552260.18293564X-RAY DIFFRACTION100
4.4659-4.62540.23391840.17443575X-RAY DIFFRACTION100
4.6254-4.81040.19551990.16923565X-RAY DIFFRACTION99
4.8104-5.02920.20691780.17533571X-RAY DIFFRACTION100
5.0292-5.2940.21672010.19323534X-RAY DIFFRACTION100
5.294-5.62520.21011740.18963604X-RAY DIFFRACTION100
5.6252-6.05880.26442080.20683546X-RAY DIFFRACTION100
6.0588-6.66720.25671780.20963563X-RAY DIFFRACTION100
6.6672-7.62880.20011710.20473586X-RAY DIFFRACTION99
7.6288-9.59950.22431790.17353497X-RAY DIFFRACTION98
9.5995-48.80690.1781490.18943496X-RAY DIFFRACTION97

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