+Open data
-Basic information
Entry | Database: PDB / ID: 7tax | ||||||
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Title | Cryo-EM structure of the Csy-AcrIF24-promoter DNA complex | ||||||
Components |
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Keywords | HYDROLASE/RNA/DNA / Csy / Cascade / CRISPR / anti-CRISPR / AcrIF24 / HYDROLASE-RNA-DNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||
Biological species | Pseudomonas (RNA similarity group I) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Mukherjee, I.A. / Chang, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Chem Biol / Year: 2022 Title: Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor. Authors: Indranil Arun Mukherjee / Clinton Gabel / Nicholas Noinaj / Joseph Bondy-Denomy / Leifu Chang / Abstract: Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure ...Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure and mechanism of AcrIF24, an Acr protein that inhibits the type I-F CRISPR-Cas system from Pseudomonas aeruginosa. AcrIF24 is a homodimer that associates with two copies of the surveillance complex (Csy) and prevents the hybridization between CRISPR RNA and target DNA. Furthermore, AcrIF24 functions as an anti-CRISPR-associated (Aca) protein to repress the transcription of the acrIF23-acrIF24 operon. Alone or in complex with Csy, AcrIF24 is capable of binding to the acrIF23-acrIF24 promoter DNA with nanomolar affinity. The structure of a Csy-AcrIF24-promoter DNA complex at 2.7 Å reveals the mechanism for transcriptional suppression. Our results reveal that AcrIF24 functions as an Acr-Aca fusion protein, and they extend understanding of the diverse mechanisms used by Acr proteins. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tax.cif.gz | 619.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tax.ent.gz | 503 KB | Display | PDB format |
PDBx/mmJSON format | 7tax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tax_validation.pdf.gz | 945.8 KB | Display | wwPDB validaton report |
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Full document | 7tax_full_validation.pdf.gz | 973.8 KB | Display | |
Data in XML | 7tax_validation.xml.gz | 86.6 KB | Display | |
Data in CIF | 7tax_validation.cif.gz | 136.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/7tax ftp://data.pdbj.org/pub/pdb/validation_reports/ta/7tax | HTTPS FTP |
-Related structure data
Related structure data | 25789MC 7t3jC 7t3kC 7t3lC 7tawC 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
-CRISPR-associated ... , 2 types, 2 molecules AC
#1: Protein | Mass: 49194.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: csy1, PA14_33330 / Production host: Escherichia (bacteria) / References: UniProt: Q02ML9 |
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#3: Protein | Mass: 21427.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: cas6f, csy4, PA14_33300 / Production host: Escherichia (bacteria) References: UniProt: Q02MM2, Hydrolases; Acting on ester bonds |
-CRISPR type I-F/YPEST-associated protein ... , 2 types, 7 molecules BDEFGHI
#2: Protein | Mass: 36244.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) Gene: csy2, ALP65_00953, IPC1598_32520, IPC29_26970, PA52Ts2_3638, PACL_0128 Production host: Escherichia (bacteria) / References: UniProt: B3G161 |
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#4: Protein | Mass: 39778.594 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: PA52Ts2_3639 / Production host: Escherichia (bacteria) / References: UniProt: A0A444M080 |
-DNA chain , 2 types, 2 molecules YX
#7: DNA chain | Mass: 5828.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas (RNA similarity group I) |
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#8: DNA chain | Mass: 5819.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas (RNA similarity group I) |
-Protein / RNA chain , 2 types, 3 molecules JKM
#5: Protein | Mass: 24995.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Production host: Escherichia (bacteria) #6: RNA chain | | Mass: 19538.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Production host: Escherichia (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: Csy-AcrIF / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 400 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Pseudomonas (RNA similarity group I) |
Source (recombinant) | Organism: Escherichia (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3.5 mg/ml / 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: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 426924 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7JZW Accession code: 7JZW / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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