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Yorodumi- PDB-8axb: Cryo-EM structure of Cas12k-sgRNA binary complex (type V-K CRISPR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8axb | |||||||||||||||
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Title | Cryo-EM structure of Cas12k-sgRNA binary complex (type V-K CRISPR-associated transposon) | |||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / CRISPR / complex / transposition | |||||||||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / Cas12k Function and homology information | |||||||||||||||
Biological species | Scytonema hofmannii (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||||||||
Authors | Tenjo-Castano, F. / Sofos, N. / Stella, S. / Molina, R. / Pape, T. / Lopez-Mendez, B. / Stutzke, L.S. / Temperini, P. / Montoya, G. | |||||||||||||||
Funding support | Denmark, 4items
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Citation | Journal: To Be Published Title: Structural prediction of the Cas12k interaction with the transposon pre-integration complex Authors: Tenjo-Castano, F. / Sofos, N. / Stella, S. / Molina, R. / Pape, T. / Lopez-Mendez, B. / Stutzke, L.S. / Temperini, P. / Montoya, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8axb.cif.gz | 226.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8axb.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 8axb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/8axb ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8axb | HTTPS FTP |
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-Related structure data
Related structure data | 15698MC 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
#1: Protein | Mass: 74738.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytonema hofmannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8M0FGU0 |
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#2: RNA chain | Mass: 84006.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytonema hofmannii (bacteria) / Production host: Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-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: Binary complex of ShCas12k bound to sgRNA. / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.159 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Scytonema hofmannii (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blotting, 4 degrees celcius |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5049 |
-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: 2228644 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180258 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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