+Open data
-Basic information
Entry | Database: PDB / ID: 6vrc | ||||||
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Title | Cryo-EM structure of Cas13(crRNA) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CRISPR-Cas system / Cas13 / TypeVI | ||||||
Function / homology | : / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / : / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a Function and homology information | ||||||
Biological species | Listeria seeligeri serovar 1/2b Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Jia, N. / Meeske, A.J. / Marraffini, L.A. / Patel, D.J. | ||||||
Citation | Journal: Science / Year: 2020 Title: A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Authors: Alexander J Meeske / Ning Jia / Alice K Cassel / Albina Kozlova / Jingqiu Liao / Martin Wiedmann / Dinshaw J Patel / Luciano A Marraffini / Abstract: The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. ...The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. However, how viruses can counteract this immunity is not known. We describe a listeriaphage (ϕLS46) encoding an anti-CRISPR protein (AcrVIA1) that inactivates the type VI-A CRISPR system of Using genetics, biochemistry, and structural biology, we found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation. Unlike inhibitors of DNA-cleaving Cas nucleases, which cause limited immunosuppression and require multiple infections to bypass CRISPR defenses, a single dose of AcrVIA1 delivered by an individual virion completely dismantles type VI-A CRISPR-mediated immunity. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vrc.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vrc.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vrc_validation.pdf.gz | 754.3 KB | Display | wwPDB validaton report |
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Full document | 6vrc_full_validation.pdf.gz | 775.5 KB | Display | |
Data in XML | 6vrc_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 6vrc_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/6vrc ftp://data.pdbj.org/pub/pdb/validation_reports/vr/6vrc | HTTPS FTP |
-Related structure data
Related structure data | 21367MC 6vrbC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 133295.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954) (bacteria) Strain: ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954 / Gene: cas13, c2c2, lse_1149 / Production host: Listeria seeligeri (bacteria) References: UniProt: P0DPB8, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 19049.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria seeligeri serovar 1/2b str. SLCC3954 (bacteria) Production host: Listeria seeligeri (bacteria) / References: GenBank: 289169617 |
-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: Cas13-crRNA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES |
Source (natural) | Organism: Listeria seeligeri (bacteria) |
Source (recombinant) | Organism: Listeria seeligeri (bacteria) |
Buffer solution | pH: 7.5 / Details: 20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM DTT |
Buffer component | Formula: Tris |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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 |
Image recording | Electron dose: 1.23 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: RELION / Version: 2.1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190543 / Symmetry type: POINT |