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Yorodumi- PDB-3flo: Crystal structure of the carboxyl-terminal domain of yeast DNA po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3flo | ||||||
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Title | Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit | ||||||
Components |
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Keywords | TRANSFERASE / Protein-protein complex / phosphoesterase fold / OB fold / Zinc-binding motif / DNA replication / Nucleus / Phosphoprotein / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information Inhibition of replication initiation of damaged DNA by RB1/E2F1 / 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 ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / 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 / telomere capping / mitotic DNA replication initiation / DNA biosynthetic process / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / DNA replication initiation / replication fork / nuclear envelope / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromatin binding / nucleotide binding / mitochondrion / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Klinge, S.N. / Pellegrini, L. | ||||||
Citation | Journal: EMBO J / Year: 2009 Title: 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. Authors: Sebastian Klinge / Rafael Núñez-Ramírez / Oscar Llorca / Luca Pellegrini / Abstract: Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol alpha, Pol delta and Pol epsilon. The conserved catalytic and regulatory B subunits associate in ...Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol alpha, Pol delta and Pol epsilon. The conserved catalytic and regulatory B subunits associate in a constitutive heterodimer that represents the functional core of all three replicative polymerases. Here, we combine X-ray crystallography and electron microscopy (EM) to describe subunit interaction and 3D architecture of heterodimeric yeast Pol alpha. The crystal structure of the C-terminal domain (CTD) of the catalytic subunit bound to the B subunit illustrates a conserved mechanism of accessory factor recruitment by replicative polymerases. The EM reconstructions of Pol alpha reveal a bilobal shape with separate catalytic and regulatory modules. Docking of the B-CTD complex in the EM reconstruction shows that the B subunit is tethered to the polymerase domain through a structured but flexible linker. Our combined findings provide a structural template for the common functional architecture of the three major replicative DNA polymerases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3flo.cif.gz | 1016.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3flo.ent.gz | 855.8 KB | Display | PDB format |
PDBx/mmJSON format | 3flo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3flo_validation.pdf.gz | 540.9 KB | Display | wwPDB validaton report |
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Full document | 3flo_full_validation.pdf.gz | 577 KB | Display | |
Data in XML | 3flo_validation.xml.gz | 92.1 KB | Display | |
Data in CIF | 3flo_validation.cif.gz | 127.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/3flo ftp://data.pdbj.org/pub/pdb/validation_reports/fl/3flo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ACEG
#1: Protein | Mass: 51962.004 Da / Num. of mol.: 4 / Fragment: UNP residues 246-705 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL12 / Plasmid: RSF1-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: P38121 |
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-DNA polymerase alpha catalytic subunit ... , 2 types, 8 molecules IJKLBDFH
#2: Protein/peptide | Mass: 273.330 Da / Num. of mol.: 4 / Fragment: N-terminal parts of chains B, D, F, H Source method: isolated from a genetically manipulated source Details: Co-expressed from the same plasmid as a protein complex Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL1, CDC17 / Plasmid: RSF1-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 #3: Protein | Mass: 23981.221 Da / Num. of mol.: 4 Fragment: Cysteine-rich C-terminal domain, UNP residues 1263-1468 Source method: isolated from a genetically manipulated source Details: Co-expressed from the same plasmid as a protein complex Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL1, CDC17 / Plasmid: RSF1-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: P13382, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 644 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAIN I, J, K, L; THE ELECTRON DENSITY MAP WAS NOT SUFFICIENTLY CLEAR TO ASSIGN UNAMBIGUOUSLY THE ...CHAIN I, J, K, L; THE ELECTRON DENSITY MAP WAS NOT SUFFICIENT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2852 |
Detector | Type: ADSC Q315R / Detector: CCD / Date: Jun 16, 2007 / Details: silicon monochromator |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2852 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→31.9 Å / Num. all: 141597 / Num. obs: 141597 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.2 / Num. unique all: 20778 / Rsym value: 0.652 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→31.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.378 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→31.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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