+Open data
-Basic information
Entry | Database: PDB / ID: 8eex | |||||||||
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Title | Cas7-11 in complex with Csx29 | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CRISPR / endonuclease / endopeptidase / 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 Function and homology information | |||||||||
Biological species | Desulfonema ishimotonii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Demircioglu, F.E. / Wilkinson, M.E. / Strecker, J. / Li, D. / Faure, G. / Macrae, R.K. / Zhang, F. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2022 Title: RNA-activated protein cleavage with a CRISPR-associated endopeptidase. Authors: Jonathan Strecker / F Esra Demircioglu / David Li / Guilhem Faure / Max E Wilkinson / Jonathan S Gootenberg / Omar O Abudayyeh / Hiroshi Nishimasu / Rhiannon K Macrae / Feng Zhang / Abstract: In prokaryotes, CRISPR-Cas systems provide adaptive immune responses against foreign genetic elements through RNA-guided nuclease activity. Recently, additional genes with non-nuclease functions have ...In prokaryotes, CRISPR-Cas systems provide adaptive immune responses against foreign genetic elements through RNA-guided nuclease activity. Recently, additional genes with non-nuclease functions have been found in genetic association with CRISPR systems, suggesting that there may be other RNA-guided non-nucleolytic enzymes. One such gene from encodes the TPR-CHAT protease Csx29, which is associated with the CRISPR effector Cas7-11. Here, we demonstrate that this CRISPR-associated protease (CASP) exhibits programmable RNA-activated endopeptidase activity against a sigma factor inhibitor to regulate a transcriptional response. Cryo-electron microscopy of an active and substrate-bound CASP complex reveals an allosteric activation mechanism that reorganizes Csx29 catalytic residues upon target RNA binding. This work reveals an RNA-guided function in nature that can be leveraged for RNA-sensing applications in vitro and in human cells. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eex.cif.gz | 437.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eex.ent.gz | 344 KB | Display | PDB format |
PDBx/mmJSON format | 8eex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eex_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8eex_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8eex_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 8eex_validation.cif.gz | 98.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/8eex ftp://data.pdbj.org/pub/pdb/validation_reports/ee/8eex | HTTPS FTP |
-Related structure data
Related structure data | 28064MC 8eeyC 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: 183844.984 Da / Num. of mol.: 1 / Mutation: D429A, D654A 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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#2: 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 | ||
#3: RNA chain | Mass: 11498.762 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) | ||
#4: Chemical | ChemComp-ZN / Has ligand of interest | N | |
-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: Cas7-11 in complex with Csx29 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Desulfonema ishimotonii (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107239 / Symmetry type: POINT |