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Open data
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Basic information
Entry | Database: PDB / ID: 8vz6 | |||||||||
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Title | PbAbiF dimer bound to ncRNA | |||||||||
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![]() | TOXIN/RNA / toxin-antitoxin / RNP / RNA-binding protein / HEPN / TOXIN / TOXIN-RNA complex | |||||||||
Function / homology | RNA / RNA (> 10)![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
![]() | Wilkinson, M.E. / Zilberzwige-Tal, S. / Altae-Tran, H. / Zhang, F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Emergence of a CRISPR RNA-guiding mechanism from a type III toxin-antitoxin system Authors: Zilberzwige-Tal, S. / Altae-Tran, H. / Kannan, S. / Wilkinson, M.E. / Vo, S.C. / Shmakov, S. / Yao, C.J. / Strebinger, D. / Edmonds, K.K. / Mears, K.S. / Makarova, K.S. / Macrae, R.K. / Koonin, E.V. / Zhang, 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 | ![]() | 161.1 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 43682MC 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
#1: Protein | Mass: 35008.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand + Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: RNA chain | Mass: 15954.489 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand + Source: (gene. exp.) ![]() Production host: ![]() ![]() Has protein modification | 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
Component | Name: AbiF RNP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.1 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 Details: 10 mM HEPES-KOH pH 7.9, 250 mM potassium acetate, 2.5 mM magnesium acetate, 5 mM beta-mercaptoethanol, 5 mM desthiobiotin |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.69 sec. / Electron dose: 42.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4272 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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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: 1142600 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12790 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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