+Open data
-Basic information
Entry | Database: PDB / ID: 7xsp | ||||||
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Title | Structure of gRAMP-target RNA | ||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA / IMMUNE SYSTEM-RNA complex | ||||||
Function / homology | CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA / RNA (> 10) / RAMP superfamily protein Function and homology information | ||||||
Biological species | Candidatus Scalindua brodae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
Authors | Feng, Y. / Zhang, L.X. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Cell / Year: 2022 Title: Target RNA activates the protease activity of Craspase to confer antiviral defense. Authors: Xi Liu / Laixing Zhang / Hao Wang / Yu Xiu / Ling Huang / Zhengyu Gao / Ningning Li / Feixue Li / Weijia Xiong / Teng Gao / Yi Zhang / Maojun Yang / Yue Feng / Abstract: In the type III-E CRISPR-Cas system, a Cas effector (gRAMP) is associated with a TPR-CHAT to form Craspase (CRISPR-guided caspase). However, both the structural features of gRAMP and the immunity ...In the type III-E CRISPR-Cas system, a Cas effector (gRAMP) is associated with a TPR-CHAT to form Craspase (CRISPR-guided caspase). However, both the structural features of gRAMP and the immunity mechanism remain unknown for this system. Here, we report structures of gRAMP-crRNA and gRAMP:cRNA:target RNA as well as structures of Craspase and Craspase complexed with cognate target RNA (CTR) or non-cognate target RNA (NTR). Importantly, the 3' anti-tag region of NTR and CTR binds at two distinct channels in Craspase, and CTR with a non-complementary 3' anti-tag induces a marked conformational change of the TPR-CHAT, which allosterically activates its protease activity to cleave an ancillary protein Csx30. This cleavage then triggers an abortive infection as the antiviral strategy of the type III-E system. Together, our study provides crucial insights into both the catalytic mechanism of the gRAMP and the immunity mechanism of the type III-E system. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xsp.cif.gz | 267 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xsp.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/7xsp ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xsp | HTTPS FTP |
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-Related structure data
Related structure data | 33430MC 7xsoC 7xsqC 7xsrC 7xssC 7xt4C 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: 197823.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Using a different transcription start point, the protein has additional five residues in its N-terminus. Source: (gene. exp.) Candidatus Scalindua brodae (bacteria) / Gene: SCABRO_02597 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0EGF3 | ||
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#2: RNA chain | Mass: 12319.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Candidatus Scalindua brodae (bacteria) | ||
#3: RNA chain | Mass: 23741.119 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) | ||
#4: 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 |
-Sample preparation
Component | Name: gRAMP-target RNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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: OTHER |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1700 nm |
Image recording | Electron dose: 50 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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274680 / Symmetry type: POINT |