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Yorodumi- PDB-7jzz: Cryo-EM structure of CRISPR-Cas surveillance complex with AcrIF14 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jzz | ||||||
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Title | Cryo-EM structure of CRISPR-Cas surveillance complex with AcrIF14 | ||||||
Components |
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Keywords | HYDROLASE/RNA / CRISPR / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) unidentified (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Chang, L. / Li, Z. / Gabel, C. | ||||||
Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14. Authors: Clinton Gabel / Zhuang Li / Heng Zhang / Leifu Chang / Abstract: CRISPR-Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins ...CRISPR-Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins are produced by MGEs to counteract CRISPR-Cas systems and can be used to regulate genome editing by CRISPR techniques. Here, we report the cryo-EM structures of three type I-F Acr proteins, AcrIF4, AcrIF7 and AcrIF14, bound to the type I-F CRISPR-Cas surveillance complex (the Csy complex) from Pseudomonas aeruginosa. AcrIF4 binds to an unprecedented site on the C-terminal helical bundle of Cas8f subunit, precluding conformational changes required for activation of the Csy complex. AcrIF7 mimics the PAM duplex of target DNA and is bound to the N-terminal DNA vise of Cas8f. Two copies of AcrIF14 bind to the thumb domains of Cas7.4f and Cas7.6f, preventing hybridization between target DNA and the crRNA. Our results reveal structural detail of three AcrIF proteins, each binding to a different site on the Csy complex for inhibiting degradation of MGEs. | ||||||
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 | 7jzz.cif.gz | 537 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzz.ent.gz | 436.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jzz_validation.pdf.gz | 848.3 KB | Display | wwPDB validaton report |
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Full document | 7jzz_full_validation.pdf.gz | 872.8 KB | Display | |
Data in XML | 7jzz_validation.xml.gz | 76.6 KB | Display | |
Data in CIF | 7jzz_validation.cif.gz | 121.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzz ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzz | HTTPS FTP |
-Related structure data
Related structure data | 22585MC 7jzwC 7jzxC 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
-Protein , 3 types, 9 molecules ADEFGHIJK
#1: Protein | Mass: 49194.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csy1, PA14_33330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02ML9 | ||
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#4: Protein | Mass: 37579.273 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: EQH76_13805, F7O93_18150, NCTC13437_01527, NCTC13619_03982 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A444M080, UniProt: Q02MM1*PLUS #5: Protein | Mass: 14297.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0R6PCL0*PLUS |
-Type I-F CRISPR-associated ... , 2 types, 2 molecules BC
#2: Protein | Mass: 36244.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: csy2, ALP65_00953, EQH76_13810, FCG96_17775, PACL_0128 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3G161, UniProt: Q02MM0*PLUS |
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#3: Protein | Mass: 21675.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cas6f, F7O93_18155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A643HZS6, UniProt: Q02MM2*PLUS |
-RNA chain , 1 types, 1 molecules M
#6: RNA chain | Mass: 19538.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 313291946 |
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-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: CRISPR-Cas complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
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: BRIGHT FIELD |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226089 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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