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- EMDB-42992: DNA elongation complex (configuration 1) of Xenopus laevis DNA po... -
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Open data
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Basic information
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Title | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
![]() | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
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![]() | Primase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / REPLICATION / 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 | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.06 Å | ||||||||||||
![]() | Mullins EA / Durie CL / Ohi MD / Chazin WJ / Eichman BF | ||||||||||||
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 EA / Salay LE / Durie CL / Bradley NP / Jackman JE / Ohi MD / Chazin WJ / Eichman BF | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 909.9 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.4 KB 28.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 2.4 KB | Display | ![]() |
Images | ![]() | 28 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Others | ![]() ![]() | 950 KB 950.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v6iMC ![]() 8g99C ![]() 8g9fC ![]() 8g9lC ![]() 8g9nC ![]() 8g9oC ![]() 8ucuC ![]() 8ucvC ![]() 8ucwC ![]() 8v5mC ![]() 8v5nC ![]() 8v5oC ![]() 8v6gC ![]() 8v6hC ![]() 8v6jC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||||||||||
Voxel size | X=Y=Z: 5.11875 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: DNA elongation complex (configuration 1) of Xenopus laevis...
File | emd_42992_half_map_1.map | ||||||||||||
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Annotation | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase (half 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: DNA elongation complex (configuration 1) of Xenopus laevis...
File | emd_42992_half_map_2.map | ||||||||||||
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Annotation | DNA elongation complex (configuration 1) of Xenopus laevis DNA polymerase alpha-primase (half 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Polymerase alpha-primase with a DNA elongation substrate
+Supramolecule #1: Polymerase alpha-primase with a DNA elongation substrate
+Supramolecule #2: Polymerase alpha
+Supramolecule #3: Primase
+Supramolecule #4: DNA elongation substrate
+Macromolecule #1: DNA polymerase alpha catalytic subunit
+Macromolecule #2: DNA polymerase alpha subunit B
+Macromolecule #3: DNA primase large subunit
+Macromolecule #4: DNA primase
+Macromolecule #5: DNA template
+Macromolecule #6: RNA-DNA primer
+Macromolecule #7: ZINC ION
+Macromolecule #8: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 3 / Number real images: 13641 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 45000 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | ![]() PDB-8v6i: |