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Yorodumi- EMDB-36225: Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36225 | |||||||||
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Title | Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | II-A type anti-CRISPR protein / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) / Staphylococcus delphini (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.82 Å | |||||||||
Authors | Deng X / Wang Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer Authors: Deng X / Wang Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36225.map.gz | 88.9 MB | EMDB map data format | |
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Header (meta data) | emd-36225-v30.xml emd-36225.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_36225.png | 130.4 KB | ||
Filedesc metadata | emd-36225.cif.gz | 6.3 KB | ||
Others | emd_36225_half_map_1.map.gz emd_36225_half_map_2.map.gz | 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36225 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36225 | HTTPS FTP |
-Related structure data
Related structure data | 8jg9MC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36225.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36225_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36225_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SaCas9-sgRNA-AcrIIA15-promoter DNA complex
+Supramolecule #1: SaCas9-sgRNA-AcrIIA15-promoter DNA complex
+Supramolecule #2: SaCas9
+Supramolecule #3: sgRNA
+Supramolecule #4: AcrIIA15
+Supramolecule #5: DNA
+Macromolecule #1: CRISPR-associated endonuclease Cas9
+Macromolecule #3: AcrIIA15
+Macromolecule #2: sgRNA
+Macromolecule #4: DNA (25-MER)
+Macromolecule #5: DNA (25-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72182 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8jg9: |