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- PDB-6w1x: Cryo-EM structure of anti-CRISPR AcrIF9, bound to the type I-F cr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w1x | ||||||||||||
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Title | Cryo-EM structure of anti-CRISPR AcrIF9, bound to the type I-F crRNA-guided CRISPR surveillance complex | ||||||||||||
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![]() | IMMUNE SYSTEM/RNA / type I-F CRISPR RNA-guided surveillance complex / Csy complex / IMMUNE SYSTEM-RNA complex | ||||||||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
![]() | Hirschi, M. / Santiago-Frangos, A. / Wilkinson, R. / Golden, S.M. / Wiedenheft, B. / Lander, G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex. Authors: Marscha Hirschi / Wang-Ting Lu / Andrew Santiago-Frangos / Royce Wilkinson / Sarah M Golden / Alan R Davidson / Gabriel C Lander / Blake Wiedenheft / ![]() ![]() Abstract: Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of ...Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 504 KB | Display | ![]() |
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PDB format | ![]() | 399.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21516MC ![]() 6whiC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-CRISPR-associated protein ... , 2 types, 7 molecules ACDEFGH
#1: Protein | Mass: 49194.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Protein | Mass: 39778.594 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein , 3 types, 4 molecules BLIJ
#2: Protein | Mass: 36244.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: csy2, ALP65_00953, EQH76_13810, FCG96_17775, PACL_0128 Production host: ![]() ![]() |
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#5: Protein | Mass: 21427.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q02MM2, Hydrolases; Acting on ester bonds |
#6: Protein | Mass: 7863.849 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 1 types, 1 molecules M
#4: RNA chain | Mass: 19265.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: unspecified / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 13.2 sec. / Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1653 |
Image scans | Movie frames/image: 66 |
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Processing
EM software | Name: Leginon / Category: image acquisition |
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CTF correction | Type: NONE |
Particle selection | Num. of particles selected: 1571636 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285707 / Symmetry type: POINT |