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Yorodumi- EMDB-33679: CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33679 | |||||||||
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Title | CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in complex with TPR-CHAT protease bound to non-self RNA target | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | CHAT domain / CHAT domain / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RAMP superfamily protein / CHAT domain protein Function and homology information | |||||||||
Biological species | Candidatus Scalindua brodae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 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: Cui N / Zhang JT / Li Z / Liu XY / Wang C / Huang H / Jia N | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33679.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-33679-v30.xml emd-33679.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
Images | emd_33679.png | 74.4 KB | ||
Masks | emd_33679_msk_1.map | 64 MB | Mask map | |
Others | emd_33679_half_map_1.map.gz emd_33679_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33679 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33679 | HTTPS FTP |
-Related structure data
Related structure data | 7y83MC 7y80C 7y81C 7y82C 7y84C 7y85C 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_33679.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_33679_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33679_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33679_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: Non-self RNA target
+Supramolecule #5: TPR-CHAT
+Macromolecule #1: RAMP superfamily protein
+Macromolecule #4: CHAT domain protein
+Macromolecule #2: crRNA
+Macromolecule #3: non-self RNA
+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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53439 |