+Open data
-Basic information
Entry | Database: PDB / ID: 7yhs | ||||||
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Title | Structure of Csy-AcrIF4-dsDNA | ||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA/DNA / IMMUNE SYSTEM-RNA-DNA complex | ||||||
Function / homology | Function and homology information CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
Authors | Feng, Y. / Zhang, L.X. | ||||||
Funding support | China, 1items
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Citation | Journal: J Biol Chem / Year: 2022 Title: Anti-CRISPR protein AcrIF4 inhibits the type I-F CRISPR-Cas surveillance complex by blocking nuclease recruitment and DNA cleavage. Authors: Zhengyu Gao / Laixing Zhang / Zihao Ge / Hao Wang / Yourun Yue / Zhuobing Jiang / Xin Wang / Chenying Xu / Yi Zhang / Maojun Yang / Yue Feng / Abstract: The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides prokaryotes with protection against mobile genetic elements such as phages. In turn, phages deploy anti- ...The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides prokaryotes with protection against mobile genetic elements such as phages. In turn, phages deploy anti-CRISPR (Acr) proteins to evade this immunity. AcrIF4, an Acr targeting the type I-F CRISPR-Cas system, has been reported to bind the crRNA-guided surveillance (Csy) complex. However, it remains controversial whether AcrIF4 inhibits target DNA binding to the Csy complex. Here, we present structural and mechanistic studies into AcrIF4, exploring its unique anti-CRISPR mechanism. While the Csy-AcrIF4 complex displays decreased affinity for target DNA, it is still able to bind the DNA. Our structural and functional analyses of the Csy-AcrIF4-dsDNA complex revealed that AcrIF4 binding prevents rotation of the helical bundle of the Cas8f subunit induced by dsDNA binding, therefore resulting in failure of nuclease Cas2/3 recruitment and DNA cleavage. Overall, our study provides an interesting example of attack on the nuclease recruitment event by an Acr, but not conventional mechanisms of blocking binding of target DNA. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yhs.cif.gz | 553.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yhs.ent.gz | 443.3 KB | Display | PDB format |
PDBx/mmJSON format | 7yhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yhs_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yhs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7yhs_validation.xml.gz | 86.5 KB | Display | |
Data in CIF | 7yhs_validation.cif.gz | 136.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/7yhs ftp://data.pdbj.org/pub/pdb/validation_reports/yh/7yhs | HTTPS FTP |
-Related structure data
Related structure data | 33837MC 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
-Protein , 5 types, 10 molecules ACDFGHIEJL
#1: Protein | Mass: 49313.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WP_004343803.1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csy1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A8DDU9 | ||||||
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#2: Protein | Mass: 37623.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A659BSG0 #3: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: B3G161 #4: Protein | | Mass: 11115.526 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WP_016068584.1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) #5: Protein | | Mass: 21429.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WP_004343806.1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) |
-RNA chain , 1 types, 1 molecules M
#6: RNA chain | Mass: 19265.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 313291946 |
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-DNA chain , 2 types, 2 molecules NO
#7: DNA chain | Mass: 16708.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 1910818228 |
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#8: DNA chain | Mass: 16574.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 1910818228 |
-Details
Has ligand of interest | Y |
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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
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||
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: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1700 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117510 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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