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Yorodumi- 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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Keywords | CRISPR-Cas / Effector complex / nuclease / cyclic oligo-adenylate synthase / ANTIVIRAL PROTEIN | ||||||||||||
| Function / homology | Function and homology information | ||||||||||||
| Biological species | ![]() Sulfolobus islandicus REY15A (archaea) / ![]() Sulfolobus islandicus (strain REY15A) (archaea) | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.41 Å | ||||||||||||
Authors | Sofos N / Montoya G | ||||||||||||
| Funding support | Denmark, 3 items
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Citation | Journal: Mol Cell / Year: 2020Title: 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. | ||||||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_10117.map.gz | 442.3 MB | EMDB map data format | |
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| Header (meta data) | emd-10117-v30.xml emd-10117.xml | 30.3 KB 30.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_10117_fsc.xml | 17.9 KB | Display | FSC data file |
| Images | emd_10117.png | 22.4 KB | ||
| Filedesc metadata | emd-10117.cif.gz | 8.6 KB | ||
| Others | emd_10117_half_map_1.map.gz emd_10117_half_map_2.map.gz | 109.1 MB 109.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10117 | HTTPS FTP |
-Validation report
| Summary document | emd_10117_validation.pdf.gz | 831.4 KB | Display | EMDB validaton report |
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| Full document | emd_10117_full_validation.pdf.gz | 830.9 KB | Display | |
| Data in XML | emd_10117_validation.xml.gz | 25.9 KB | Display | |
| Data in CIF | emd_10117_validation.cif.gz | 34 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10117 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10117 | 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 | EMDB (EBI/PDBe) / EMDataResource |
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Map
| File | Download / File: emd_10117.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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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-Half map: #2
| File | emd_10117_half_map_2.map | ||||||||||||
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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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Processing | 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 - Time: 60 sec. / 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: FIELD EMISSION GUN |
| 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: |
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About Yorodumi


Keywords
Sulfolobus islandicus REY15A (archaea)
Authors
Denmark, 3 items
Citation
UCSF Chimera
















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