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- PDB-8v6g: DNA initiation complex (configuration 1) of Xenopus laevis DNA po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v6g | ||||||||||||
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Title | DNA initiation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
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![]() | REPLICATION / TRANSFERASE / Primase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / TRANSFERASE-DNA-RNA complex | ||||||||||||
Function / homology | ![]() alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation ...alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.16 Å | ||||||||||||
![]() | Mullins, E.A. / Durie, C.L. / Ohi, M.D. / Chazin, W.J. / Eichman, B.F. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Authors: Elwood A Mullins / Lauren E Salay / Clarissa L Durie / Noah P Bradley / Jane E Jackman / Melanie D Ohi / Walter J Chazin / Brandt F Eichman / ![]() Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is ...The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase. #1: ![]() Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase Authors: Mullins, E.A. / Salay, L.E. / Durie, C.L. / Bradley, N.P. / Jackman, J.E. / Ohi, M.D. / Chazin, W.J. / Eichman, B.F. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 921.1 KB | Display | ![]() |
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PDB format | ![]() | 748.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 42990MC ![]() 8g99C ![]() 8g9fC ![]() 8g9lC ![]() 8g9nC ![]() 8g9oC ![]() 8ucuC ![]() 8ucvC ![]() 8ucwC ![]() 8v5mC ![]() 8v5nC ![]() 8v5oC ![]() 8v6hC ![]() 8v6iC ![]() 8v6jC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA polymerase alpha ... , 2 types, 2 molecules AB
#1: Protein | Mass: 129009.414 Da / Num. of mol.: 1 / Fragment: UNP residues 335-1458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 67194.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 59673.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 49356.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain / RNA chain , 2 types, 2 molecules EF
#5: DNA chain | Mass: 15458.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: RNA chain | Mass: 2999.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/ZN.gif)
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#7: Chemical | #8: Chemical | ChemComp-DGT / | #9: Chemical | #10: Chemical | ChemComp-SF4 / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 12845 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 11200341 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9156 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building |
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