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- EMDB-27258: Human DNA polymerase-alpha/primase elongation complex II bound to... -
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Open data
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Basic information
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Title | Human DNA polymerase-alpha/primase elongation complex II bound to primer/template | |||||||||
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![]() | DNA replication / human DNA polymerase alpha/primase / human primosome / elongation complex / REPLICATION | |||||||||
Function / homology | ![]() positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / regulation of type I interferon production ...positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / regulation of type I interferon production / Processive synthesis on the lagging strand / DNA primase activity / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / protein import into nucleus / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
![]() | He Q / Baranovskiy A / Lim C / Tahirov T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of human primosome elongation complexes. Authors: Qixiang He / Andrey G Baranovskiy / Lucia M Morstadt / Alisa E Lisova / Nigar D Babayeva / Benjamin L Lusk / Ci Ji Lim / Tahir H Tahirov / ![]() Abstract: The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. ...The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.5 KB 27.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 120.2 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 816.1 KB | Display | ![]() |
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Full document | ![]() | 815.7 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d9dMC ![]() 8d96C C: citing same article ( M: atomic model generated by this map |
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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 | Unsharpened and flipped map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_27258_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_27258_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Elongation complex II of human DNA polymerase alpha/primase bound...
+Supramolecule #1: Elongation complex II of human DNA polymerase alpha/primase bound...
+Macromolecule #1: DNA primase small subunit
+Macromolecule #2: DNA primase large subunit
+Macromolecule #3: DNA polymerase alpha catalytic subunit
+Macromolecule #4: DNA polymerase alpha subunit B
+Macromolecule #5: DNA/RNA (5'-D(*(GTP))-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
+Macromolecule #6: DNA (5'-D(*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*...
+Macromolecule #7: ZINC ION
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13243 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||||||
Output model | ![]() PDB-8d9d: |