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- PDB-6shb: Cryo-EM structure of the Type III-B Cmr-beta bound to cognate tar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6shb | ||||||||||||
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Title | Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 1, in the presence of ssDNA | ||||||||||||
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![]() | ANTIVIRAL PROTEIN / CRISPR-Cas / Effector complex / nuclease / cyclic oligo-adenylate synthase | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||||||||
![]() | Sofos, N. / Montoya, G. / Stella, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas. Authors: Nicholas Sofos / Mingxia Feng / Stefano Stella / Tillmann Pape / Anders Fuglsang / Jinzhong Lin / Qihong Huang / Yingjun Li / Qunxin She / Guillermo Montoya / ![]() ![]() Abstract: Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) ...Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific single-stranded RNA (ssRNA) hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β, unveiling how binding of the target RNA regulates the Cmr2 activities. Cryoelectron microscopy (cryo-EM) analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA-bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5' tag in the CRISPR RNAs (crRNA) and the 3' antitag of the target RNA activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self- versus non-self-recognition. These findings highlight the diverse defense strategies of type III complexes. #1: ![]() Title: Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas Authors: Sofos, N. / Feng, M. / Stella, S. / Pape, T. / Fuglsang, A. / Lin, J. / Huang, Q. / Li, Y. / She, Q. / Montoya, G. | ||||||||||||
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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10197MC ![]() 6s6bC ![]() 6s8bC ![]() 6s8eC ![]() 6s91C ![]() 6sh8C ![]() 6sicC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-CRISPR-associated protein, ... , 3 types, 5 molecules ABCKH
#1: Protein | Mass: 17961.834 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: F0NDX5 #8: Protein | | Mass: 120856.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: F0NDX2 #9: Protein | | Mass: 36008.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: F0NDX1 |
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-CRISPR-associated RAMP protein, ... , 2 types, 5 molecules DEFGI
#2: Protein | Mass: 32322.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Asp31 mutated to Ala Source: (gene. exp.) ![]() ![]() Gene: SiRe_0602 / Production host: ![]() ![]() #3: Protein | | Mass: 33945.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal histidine-tag Source: (gene. exp.) ![]() ![]() Gene: SiRe_0599 / Production host: ![]() ![]() |
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-Protein , 2 types, 27 molecules JLMNOPQRSTWXlmnopqrstwxZzYy
#4: Protein | Mass: 55388.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: F0NDX4 |
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#7: Protein | Mass: 19705.607 Da / Num. of mol.: 26 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: F0NDX7 |
-RNA chain , 2 types, 2 molecules UV
#5: RNA chain | Mass: 14704.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: RNA chain | Mass: 16409.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
-Non-polymers , 3 types, 6 molecules ![](data/chem/img/ZN.gif)
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#10: Chemical | ChemComp-ZN / | ||
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#11: Chemical | #12: Chemical | |
-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 |
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Sample preparation
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Molecular weight | Value: 0.9 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: 5 mA (Leica EM ACE200) / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3-4 s blotting before plunging |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1700 nm / Cs: 2.1 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40 sec. / Electron dose: 41 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5298 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 429000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65610 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient |