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- EMDB-10117: 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: EMDB / ID: EMD-10117 | ||||||||||||
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Title | Cryo-EM structure of the Type III-B Cmr-beta bound to cognate target RNA and AMPPnP, state 1 | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.41 Å | ||||||||||||
![]() | Sofos N / Montoya G | ||||||||||||
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. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 442.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.2 KB 30.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.9 KB | Display | ![]() |
Images | ![]() | 22.4 KB | ||
Others | ![]() ![]() | 109.1 MB 109.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s8bMC ![]() 6s6bC ![]() 6s8eC ![]() 6s91C ![]() 6sh8C ![]() 6shbC ![]() 6sicC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_10117_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10117_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPn...
+Supramolecule #1: Type III-B Cmr-beta ternary complex, cognate target RNA and AMPPn...
+Macromolecule #1: CRISPR-associated protein, Cmr5 family
+Macromolecule #2: CRISPR-associated RAMP protein, Cmr4 family
+Macromolecule #3: CRISPR-associated protein, Cmr3 family
+Macromolecule #4: CRISPR-associated RAMP protein, Cmr6 family
+Macromolecule #5: Cmr1
+Macromolecule #8: CRISPR-associated protein Cmrx
+Macromolecule #9: CRISPR-associated protein, Cmr2 family
+Macromolecule #6: Cognate target RNA (46-mer)
+Macromolecule #7: crRNA
+Macromolecule #10: ZINC ION
+Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #12: MANGANESE (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.8 mg/mL | |||||||||||||||
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Buffer | pH: 6 Component:
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Grid | Model: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 5 mA. Model: Leica EM ACE200 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 s blotting before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3912 / Average exposure time: 40.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-6s8b: |