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Yorodumi- PDB-8gs2: Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gs2 | |||||||||
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Title | Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CRISPR / RNase / RNA BINDING PROTEIN-RNA COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Desulfonema ishimotonii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Kato, K. / Okazaki, S. / Ishikawa, J. / Isayama, Y. / Nishizawa, T. / Nishimasu, H. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Science / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gs2.cif.gz | 443.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gs2.ent.gz | 343.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gs2_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8gs2_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8gs2_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 8gs2_validation.cif.gz | 90.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/8gs2 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/8gs2 | HTTPS FTP |
-Related structure data
Related structure data | 34218MC 7y9xC 7y9yC 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
-RNA chain , 2 types, 2 molecules RD
#1: RNA chain | Mass: 30532.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfonema ishimotonii (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 10662.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Desulfonema ishimotonii (bacteria) |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 185603.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfonema ishimotonii (bacteria) / Gene: DENIS_1082 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A401FT36 |
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#4: Protein | Mass: 88311.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfonema ishimotonii (bacteria) / Gene: DENIS_1081 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A401FT52 |
-Non-polymers , 3 types, 7 molecules
#5: Chemical | ChemComp-C5P / | ||
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#6: Chemical | #7: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | Y |
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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 |
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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 |
-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: 1500 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 76.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71543 / Symmetry type: POINT |