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Yorodumi- PDB-7y83: CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y83 | ||||||
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Title | CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in complex with TPR-CHAT protease bound to non-self RNA target | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/RNA / Nuclease / STRUCTURAL PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Candidatus Scalindua brodae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
Authors | Zhang, J.T. / Cui, N. / Huang, H.D. / Jia, N. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase. Authors: Ning Cui / Jun-Tao Zhang / Zhuolin Li / Xiao-Yu Liu / Chongyuan Wang / Hongda Huang / Ning Jia / Abstract: The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. ...The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMP and gRAMP-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions -1 and -2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y83.cif.gz | 432.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y83.ent.gz | 331.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y83_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7y83_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7y83_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 7y83_validation.cif.gz | 95.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y83 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y83 | HTTPS FTP |
-Related structure data
Related structure data | 33679MC 7y80C 7y81C 7y82C 7y84C 7y85C 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
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 198652.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02597 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EGF3 |
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#4: Protein | Mass: 85523.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02601 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EKL4 |
-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 35432.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Production host: Escherichia coli (E. coli) |
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#3: RNA chain | Mass: 18097.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Candidatus Scalindua brodae (bacteria) |
-Non-polymers , 2 types, 5 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-MG / | |
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-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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53439 / Symmetry type: POINT |