+Open data
-Basic information
Entry | Database: PDB / ID: 8dc2 | |||||||||
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Title | Cryo-EM structure of CasLambda (Cas12l) bound to crRNA and DNA | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / CRISPR / RNA Binding Protein / DNA binding protein / phage / viral protein / enzyme / ribonucleoprotein / RNA BINDING PROTEIN-RNA-DNA complex | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | uncultured virus (environmental samples) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Al-Shayeb, B. / Skopintsev, P. / Soczek, K. / Doudna, J. | |||||||||
Funding support | United States, Switzerland, 2items
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Citation | Journal: Cell / Year: 2022 Title: Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Authors: Basem Al-Shayeb / Petr Skopintsev / Katarzyna M Soczek / Elizabeth C Stahl / Zheng Li / Evan Groover / Dylan Smock / Amy R Eggers / Patrick Pausch / Brady F Cress / Carolyn J Huang / Brian ...Authors: Basem Al-Shayeb / Petr Skopintsev / Katarzyna M Soczek / Elizabeth C Stahl / Zheng Li / Evan Groover / Dylan Smock / Amy R Eggers / Patrick Pausch / Brady F Cress / Carolyn J Huang / Brian Staskawicz / David F Savage / Steven E Jacobsen / Jillian F Banfield / Jennifer A Doudna / Abstract: CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are ...CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dc2.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dc2.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dc2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8dc2_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8dc2_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 8dc2_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/8dc2 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dc2 | HTTPS FTP |
-Related structure data
Related structure data | 27320MC 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: 87337.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured virus (environmental samples) Production host: Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 16483.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) |
#3: DNA chain | Mass: 14296.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) |
#4: DNA chain | Mass: 14371.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) |
-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: CasLambda-crRNA-dsDNA ternary structure / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: uncultured virus (environmental samples) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 369389 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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