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Yorodumi- PDB-6iv6: Cryo-EM structure of AcrVA5-acetylated MbCas12a in complex with crRNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iv6 | |||||||||
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Title | Cryo-EM structure of AcrVA5-acetylated MbCas12a in complex with crRNA | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA / enzyme / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex | |||||||||
Function / homology | Function and homology information CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain Similarity search - Domain/homology | |||||||||
Biological species | Moraxella bovoculi (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Dong, L. / Li, N. / Guan, X. / Zhu, Y. / Gao, N. / Huang, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: An anti-CRISPR protein disables type V Cas12a by acetylation. Authors: Liyong Dong / Xiaoyu Guan / Ningning Li / Fan Zhang / Yuwei Zhu / Kuan Ren / Ling Yu / Fengxia Zhou / Zhifu Han / Ning Gao / Zhiwei Huang / Abstract: Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. The mechanisms for the inhibition of type I and type II systems by anti-CRISPRs have been elucidated. However, it has remained ...Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. The mechanisms for the inhibition of type I and type II systems by anti-CRISPRs have been elucidated. However, it has remained unknown how the type V CRISPR-Cas12a (Cpf1) system is inhibited by anti-CRISPRs. Here we identify the anti-CRISPR protein AcrVA5 and report the mechanisms by which it inhibits CRISPR-Cas12a. Our structural and biochemical data show that AcrVA5 functions as an acetyltransferase to modify Moraxella bovoculi (Mb) Cas12a at Lys635, a residue that is required for recognition of the protospacer-adjacent motif. The AcrVA5-mediated modification of MbCas12a results in complete loss of double-stranded DNA (dsDNA)-cleavage activity. In contrast, the Lys635Arg mutation renders MbCas12a completely insensitive to inhibition by AcrVA5. A cryo-EM structure of the AcrVA5-acetylated MbCas12a reveals that Lys635 acetylation provides sufficient steric hindrance to prevent dsDNA substrates from binding to the Cas protein. Our study reveals an unprecedented mechanism of CRISPR-Cas inhibition and suggests an evolutionary arms race between phages and bacteria. | |||||||||
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 | 6iv6.cif.gz | 243.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iv6.ent.gz | 186.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iv6_validation.pdf.gz | 777.1 KB | Display | wwPDB validaton report |
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Full document | 6iv6_full_validation.pdf.gz | 786.7 KB | Display | |
Data in XML | 6iv6_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 6iv6_validation.cif.gz | 57.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6iv6 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6iv6 | HTTPS FTP |
-Related structure data
Related structure data | 9742MC 6iufC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 145253.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella bovoculi (bacteria) / Gene: AAX07_00205 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2B2X7 |
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#2: RNA chain | Mass: 18673.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
Has protein modification | 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: cpf1-crRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Moraxella bovoculi (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: NITROGEN |
-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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 81 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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