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Yorodumi- PDB-7z0z: Abortive infection DNA polymerase AbiK from Lactococcus lactis, Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z0z | |||||||||
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Title | Abortive infection DNA polymerase AbiK from Lactococcus lactis, Y44F variant | |||||||||
Components | AbiK | |||||||||
Keywords | ANTIVIRAL PROTEIN / DNA polymerase / protein-primed DNA synthesis / template-independent DNA synthesis / abortive infection | |||||||||
Function / homology | Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / metal ion binding / AbiK Function and homology information | |||||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
Authors | Figiel, M. / Gapinska, M. / Czarnocki-Cieciura, M. / Zajko, W. / Nowotny, M. | |||||||||
Funding support | Poland, European Union, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases. Authors: Małgorzata Figiel / Marta Gapińska / Mariusz Czarnocki-Cieciura / Weronika Zajko / Małgorzata Sroka / Krzysztof Skowronek / Marcin Nowotny Abstract: Abortive infection (Abi) is a bacterial antiphage defense strategy involving suicide of the infected cell. Some Abi pathways involve polymerases that are related to reverse transcriptases. They are ...Abortive infection (Abi) is a bacterial antiphage defense strategy involving suicide of the infected cell. Some Abi pathways involve polymerases that are related to reverse transcriptases. They are unique in the way they combine the ability to synthesize DNA in a template-independent manner with protein priming. Here, we report crystal and cryo-electron microscopy structures of two Abi polymerases: AbiK and Abi-P2. Both proteins adopt a bilobal structure with an RT-like domain that comprises palm and fingers subdomains and a unique helical domain. AbiK and Abi-P2 adopt a hexameric and trimeric configuration, respectively, which is unprecedented for reverse transcriptases. Biochemical experiments showed that the formation of these oligomers is required for the DNA polymerization activity. The structure of the AbiK-DNA covalent adduct visualized interactions between the 3' end of DNA and the active site and covalent attachment of the 5' end of DNA to a tyrosine residue used for protein priming. Our data reveal a structural basis of the mechanism of highly unusual template-independent protein-priming polymerases. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 7z0z.cif.gz | 845.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z0z.ent.gz | 667.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z0z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7z0z_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7z0z_validation.xml.gz | 100.6 KB | Display | |
Data in CIF | 7z0z_validation.cif.gz | 154.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z0z ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z0z | HTTPS FTP |
-Related structure data
Related structure data | 14435MC 7r06C 7r07C 7r08C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 71617.109 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: abiK / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Star / References: UniProt: Q48614 |
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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: Homohexamer of L. lactis AbiK Y44F mutant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.42 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Lactococcus lactis (lactic acid bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) / Strain: Star | |||||||||||||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.74 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.18_3845: / 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: 2306347 | ||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50340 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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