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Yorodumi- PDB-8d96: Human DNA polymerase alpha/primase elongation complex I bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d96 | |||||||||
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Title | Human DNA polymerase alpha/primase elongation complex I bound to primer/template | |||||||||
Components |
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Keywords | REPLICATION / DNA replication / human DNA polymerase alpha/primase / human primosome / elongation complex | |||||||||
Function / homology | Function and homology information positive regulation of DNA primase activity / 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 / Removal of the Flap Intermediate ...positive regulation of DNA primase activity / 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 / 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 / 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 / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | He, Q. / Baranovskiy, A. / Lim, C. / Tahirov, T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d96.cif.gz | 266.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d96.ent.gz | 193.3 KB | Display | PDB format |
PDBx/mmJSON format | 8d96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d96_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8d96_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8d96_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 8d96_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/8d96 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/8d96 | HTTPS FTP |
-Related structure data
Related structure data | 27256MC 8d9dC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules BC
#1: Protein | Mass: 58890.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 166131.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLA1, POLA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P09884, DNA-directed DNA polymerase |
-DNA/RNA hybrid / DNA chain , 2 types, 2 molecules EF
#3: DNA/RNA hybrid | Mass: 3977.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#4: DNA chain | Mass: 6760.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 3 molecules
#5: Chemical | ChemComp-SF4 / |
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#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-DTP / |
-Details
Has ligand of interest | Y |
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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 |
-Sample preparation
Component | Name: Elongation complex I of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template Type: COMPLEX Details: Smaller elongation complex solved using cryo-EM single-particle analysis Entity ID: #1-#4 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.340 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Cell: combined with SF9 cells | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification. | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 13243 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2522283 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151102 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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