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Yorodumi- EMDB-33681: CryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33681 | |||||||||
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Title | CryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with TPR-CHAT bound to self RNA target | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nuclease / STRUCTURAL PROTEIN-RNA COMPLEX | |||||||||
Function / homology | CHAT domain / CHAT domain / : / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA binding / RAMP superfamily protein / CHAT domain protein Function and homology information | |||||||||
Biological species | Candidatus Scalindua brodae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
Authors | Zhang JT / Cui N / Huang HD / Jia N | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase. Authors: Ning Cui / Jun-Tao Zhang / Zhuolin Li / Xiao-Yu Liu / Chongyuan Wang / Hongda Huang / Ning Jia / Abstract: The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. ...The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMP and gRAMP-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions -1 and -2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33681.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-33681-v30.xml emd-33681.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
Images | emd_33681.png | 84.1 KB | ||
Masks | emd_33681_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-33681.cif.gz | 7.2 KB | ||
Others | emd_33681_half_map_1.map.gz emd_33681_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33681 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33681 | HTTPS FTP |
-Validation report
Summary document | emd_33681_validation.pdf.gz | 983.3 KB | Display | EMDB validaton report |
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Full document | emd_33681_full_validation.pdf.gz | 982.9 KB | Display | |
Data in XML | emd_33681_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_33681_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33681 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33681 | HTTPS FTP |
-Related structure data
Related structure data | 7y85MC 7y80C 7y81C 7y82C 7y83C 7y84C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33681.map.gz / Format: CCP4 / Size: 64 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33681_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33681_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33681_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Type III-E CRISPR gRAMP-crRNA binary complex
+Supramolecule #1: Type III-E CRISPR gRAMP-crRNA binary complex
+Supramolecule #2: gRAMP
+Supramolecule #3: crRNA
+Supramolecule #4: Self RNA target
+Supramolecule #5: TPR-CHAT
+Macromolecule #1: RAMP superfamily protein
+Macromolecule #4: CHAT domain protein
+Macromolecule #2: crRNA
+Macromolecule #3: Self RNA target
+Macromolecule #5: ZINC ION
+Macromolecule #6: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123862 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |