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- PDB-7vtn: Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vtn | ||||||
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Title | Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex | ||||||
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![]() | RNA BINDING PROTEIN/RNA / CRISPR-Cas / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | RNA / RNA (> 10) / Uncharacterized protein![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||
![]() | Nakagawa, R. / Soumya, K. / Han, A. / Takeda, N.S. / Tomita, A. / Hirano, H. / Kusakizako, T. / Tomohiro, N. / Yamashita, K. / Feng, Z. ...Nakagawa, R. / Soumya, K. / Han, A. / Takeda, N.S. / Tomita, A. / Hirano, H. / Kusakizako, T. / Tomohiro, N. / Yamashita, K. / Feng, Z. / Nishimasu, H. / Nureki, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and engineering of the minimal type VI CRISPR-Cas13bt3. Authors: Ryoya Nakagawa / Soumya Kannan / Han Altae-Tran / Satoru N Takeda / Atsuhiro Tomita / Hisato Hirano / Tsukasa Kusakizako / Tomohiro Nishizawa / Keitaro Yamashita / Feng Zhang / Hiroshi ...Authors: Ryoya Nakagawa / Soumya Kannan / Han Altae-Tran / Satoru N Takeda / Atsuhiro Tomita / Hisato Hirano / Tsukasa Kusakizako / Tomohiro Nishizawa / Keitaro Yamashita / Feng Zhang / Hiroshi Nishimasu / Osamu Nureki / ![]() ![]() ![]() Abstract: Type VI CRISPR-Cas13 effector enzymes catalyze RNA-guided RNA cleavage and have been harnessed for various technologies, such as RNA detection, targeting, and editing. Recent studies identified ...Type VI CRISPR-Cas13 effector enzymes catalyze RNA-guided RNA cleavage and have been harnessed for various technologies, such as RNA detection, targeting, and editing. Recent studies identified Cas13bt3 (also known as Cas13X.1) as a miniature Cas13 enzyme, which can be used for knockdown and editing of target transcripts in mammalian cells. However, the action mechanism of the compact Cas13bt3 remains unknown. Here, we report the structures of the Cas13bt3-guide RNA complex and the Cas13bt3-guide RNA-target RNA complex. The structures revealed how Cas13bt3 recognizes the guide RNA and its target RNA and provided insights into the activation mechanism of Cas13bt3, which is distinct from those of the other Cas13a/d enzymes. Furthermore, we rationally engineered enhanced Cas13bt3 variants and ultracompact RNA base editors. Overall, this study improves our mechanistic understanding of the CRISPR-Cas13 enzymes and paves the way for the development of efficient Cas13-mediated transcriptome modulation technologies. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 149.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 32118MC ![]() 7vtiC 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: 90498.789 Da / Num. of mol.: 1 / Mutation: R84A, H89A, R739A, H744A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 19603.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 7984.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE | ||||||||||||||||||||||||
Crystal grow | Method: vapor diffusion, hanging drop |
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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 defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 48.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0352 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2380559 / Num. of class averages: 3 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.38→3.38 Å / Cor.coef. Fo:Fc: 0.905 / SU B: 29.392 / SU ML: 0.497 / ESU R: 0.461 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 191.023 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 7305 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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