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Yorodumi- EMDB-3454: RNA activation-independent DNA targeting by a Csm complex of the ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3454 | |||||||||
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Title | RNA activation-independent DNA targeting by a Csm complex of the Type III CRISPR-Cas system | |||||||||
Map data | Csm complex with crRNA from T.onnurineus | |||||||||
Sample |
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Biological species | Thermococcus onnurineus NA1 (archaea) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Jung TY / Song JJ / Hebert H / Woo EJ / Oh BH / Park KH / An Y | |||||||||
Citation | Journal: EMBO Rep / Year: 2017 Title: RNA activation-independent DNA targeting of the Type III CRISPR-Cas system by a Csm complex. Authors: Kwang-Hyun Park / Yan An / Tae-Yang Jung / In-Young Baek / Haemin Noh / Woo-Chan Ahn / Hans Hebert / Ji-Joon Song / Jeong-Hoon Kim / Byung-Ha Oh / Eui-Jeon Woo / Abstract: The CRISPR-Cas system is an adaptive and heritable immune response that destroys invading foreign nucleic acids. The effector complex of the Type III CRISPR-Cas system targets RNA and DNA in a ...The CRISPR-Cas system is an adaptive and heritable immune response that destroys invading foreign nucleic acids. The effector complex of the Type III CRISPR-Cas system targets RNA and DNA in a transcription-coupled manner, but the exact mechanism of DNA targeting by this complex remains elusive. In this study, an effector Csm holocomplex derived from is reconstituted with a minimalistic combination of Csm12345, and shows RNA targeting and RNA-activated single-stranded DNA (ssDNA) targeting activities. Unexpectedly, in the absence of an RNA transcript, it cleaves ssDNA containing a sequence complementary to the bound crRNA guide region in a manner dependent on the HD domain of the Csm1 subunit. This nuclease activity is blocked by a repeat tag found in the host CRISPR loci. The specific cleavage of ssDNA without a target RNA suggests a novel ssDNA targeting mechanism of the Type III system, which could facilitate the efficient and complete degradation of foreign nucleic acids. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3454.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-3454-v30.xml emd-3454.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3454_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_3454.png | 30.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3454 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3454 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3454.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Csm complex with crRNA from T.onnurineus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Csm complex with crRNA from T.onnurineus
Entire | Name: Csm complex with crRNA from T.onnurineus |
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Components |
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-Supramolecule #1: Csm complex with crRNA from T.onnurineus
Supramolecule | Name: Csm complex with crRNA from T.onnurineus / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermococcus onnurineus NA1 (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pRSFDuet-1, pETDuel-1, pACYCDuet-1 |
Molecular weight | Experimental: 280 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.025 mg/mL |
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Buffer | pH: 8 |
Staining | Type: NEGATIVE / Material: Uranyl acetate |
-Electron microscopy
Microscope | JEOL 2100F |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm |
Sample stage | Specimen holder model: JEOL |
Image recording | Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 30.0 e/Å2 |