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- PDB-7y9y: Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y9y | ||||||
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Title | Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex | ||||||
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![]() | RNA BINDING PROTEIN/RNA / CRISPR / RNase / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | CHAT domain / CHAT domain / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA / RNA (> 10) / CRISPR-associated RAMP family protein / CHAT domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||
![]() | Kato, K. / Okazaki, S. / Ishikawa, J. / Isayama, Y. / Nishizawa, T. / Nishimasu, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Authors: Kazuki Kato / Sae Okazaki / Cian Schmitt-Ulms / Kaiyi Jiang / Wenyuan Zhou / Junichiro Ishikawa / Yukari Isayama / Shungo Adachi / Tomohiro Nishizawa / Kira S Makarova / Eugene V Koonin / ...Authors: Kazuki Kato / Sae Okazaki / Cian Schmitt-Ulms / Kaiyi Jiang / Wenyuan Zhou / Junichiro Ishikawa / Yukari Isayama / Shungo Adachi / Tomohiro Nishizawa / Kira S Makarova / Eugene V Koonin / Omar O Abudayyeh / Jonathan S Gootenberg / Hiroshi Nishimasu / ![]() ![]() Abstract: The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11- ...The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNA binding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependent cleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showed that Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated by Csx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E), suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. We engineered the Cas7-11-Csx29-Csx30 system for programmable RNA sensing in mammalian cells. Overall, the Cas7-11-Csx29 effector is an RNA-dependent nuclease-protease. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.6 KB | Display | ![]() |
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PDB format | ![]() | 282.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 82.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33696MC ![]() 7y9xC ![]() 8gs2C 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: RNA chain | Mass: 12134.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
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#2: RNA chain | Mass: 8703.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: Protein | Mass: 185653.875 Da / Num. of mol.: 1 / Mutation: D429A, D654A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Protein | Mass: 88311.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#5: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
-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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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: 1500 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291630 / Symmetry type: POINT |