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Yorodumi- EMDB-21607: Internal translation of large subunit transcripts drives synthesi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21607 | |||||||||
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Title | Internal translation of large subunit transcripts drives synthesis of small subunits in type I CRISPR-Cas Cascade | |||||||||
Map data | Type I-D Cascade from Synechocystis with crRNA bound. | |||||||||
Sample |
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Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | McBride TM / Schwartz EA / Kumar A / Taylor DW / Fineran PC / Fagerlund RD | |||||||||
Citation | Journal: Mol Cell / Year: 2020 Title: Diverse CRISPR-Cas Complexes Require Independent Translation of Small and Large Subunits from a Single Gene. Authors: Tess M McBride / Evan A Schwartz / Abhishek Kumar / David W Taylor / Peter C Fineran / Robert D Fagerlund / Abstract: CRISPR-Cas adaptive immune systems provide prokaryotes with defense against viruses by degradation of specific invading nucleic acids. Despite advances in the biotechnological exploitation of select ...CRISPR-Cas adaptive immune systems provide prokaryotes with defense against viruses by degradation of specific invading nucleic acids. Despite advances in the biotechnological exploitation of select systems, multiple CRISPR-Cas types remain uncharacterized. Here, we investigated the previously uncharacterized type I-D interference complex and revealed that it is a genetic and structural hybrid with similarity to both type I and type III systems. Surprisingly, formation of the functional complex required internal in-frame translation of small subunits from within the large subunit gene. We further show that internal translation to generate small subunits is widespread across diverse type I-D, I-B, and I-C systems, which account for roughly one quarter of CRISPR-Cas systems. Our work reveals the unexpected expansion of protein coding potential from within single cas genes, which has important implications for understanding CRISPR-Cas function and evolution. | |||||||||
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_21607.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-21607-v30.xml emd-21607.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_21607.png | 24.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21607 | HTTPS FTP |
-Validation report
Summary document | emd_21607_validation.pdf.gz | 297.3 KB | Display | EMDB validaton report |
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Full document | emd_21607_full_validation.pdf.gz | 296.8 KB | Display | |
Data in XML | emd_21607_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21607 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21607 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21607.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Type I-D Cascade from Synechocystis with crRNA bound. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.61 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 : Type I-D Cascade
Entire | Name: Type I-D Cascade |
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Components |
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-Supramolecule #1: Type I-D Cascade
Supramolecule | Name: Type I-D Cascade / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 450 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.045 mg/mL |
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Buffer | pH: 7.5 |
Staining | Type: NEGATIVE / Material: uranyl acetate |
Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 70 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 57000 |
Sample stage | Specimen holder model: OTHER |