+Open data
-Basic information
Entry | Database: PDB / ID: 7we6 | ||||||
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Title | Structure of Csy-AcrIF24-dsDNA | ||||||
Components |
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Keywords | VIRAL PROTEIN / complex / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Zhang, L. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24. Authors: Lingguang Yang / Laixing Zhang / Peipei Yin / Hao Ding / Yu Xiao / Jianwei Zeng / Wenhe Wang / Huan Zhou / Qisheng Wang / Yi Zhang / Zeliang Chen / Maojun Yang / Yue Feng / Abstract: CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the ...CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7we6.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7we6.ent.gz | 872.3 KB | Display | PDB format |
PDBx/mmJSON format | 7we6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7we6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7we6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7we6_validation.xml.gz | 155.1 KB | Display | |
Data in CIF | 7we6_validation.cif.gz | 248.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/7we6 ftp://data.pdbj.org/pub/pdb/validation_reports/we/7we6 | HTTPS FTP |
-Related structure data
Related structure data | 32440MC 7dtrC 7elmC 7elnC 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 , 3 types, 16 molecules BLCDEFGHMNOPQRUV
#1: Protein | Mass: 36244.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: csy2, ALP65_00953, EQH76_13810, NCTC13437_01526, PACL_0128 Production host: Escherichia coli (E. coli) / References: UniProt: B3G161 #2: Protein | Mass: 37623.324 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: IPC1505_30680, IPC36_28835 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A659BSG0 #4: Protein | Mass: 24995.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) |
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-Type I-F CRISPR-associated ... , 2 types, 4 molecules ISAX
#3: Protein | Mass: 21429.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cas6f, DT376_16430, PA52Ts2_3640 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C6F3X3 #6: Protein | Mass: 49313.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csy1, ALP65_00954, IPC1505_30690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A8DDU9 |
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-RNA chain , 1 types, 2 molecules JT
#5: RNA chain | Mass: 19265.404 Da / Num. of mol.: 2 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, 4 molecules YKZW
#7: DNA chain | Mass: 16574.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 1910818228 #8: DNA chain | Mass: 16708.691 Da / Num. of mol.: 2 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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-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-AcrIF24 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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: 1700 nm / Nominal defocus min: 1300 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: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 474421 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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