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Yorodumi- EMDB-27142: Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27142 | |||||||||
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Title | Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cleavage Intermediate 1) | |||||||||
Map data | AcCas9 Cleavage intermediate 1 | |||||||||
Sample |
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Keywords | Cas9 / AcCas9 / Crispr / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | Function and homology information defense response to virus / endonuclease activity / DNA binding / RNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Acidothermus cellulolyticus 11B (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.21 Å | |||||||||
Authors | Rai J / Das A / Li H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Catal / Year: 2023 Title: Coupled catalytic states and the role of metal coordination in Cas9 Authors: Das A / Rai J / Roth MO / Shu Y / Medina ML / Barakat MR / Li H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27142.map.gz | 100.5 MB | EMDB map data format | |
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Header (meta data) | emd-27142-v30.xml emd-27142.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
Images | emd_27142.png | 50.6 KB | ||
Filedesc metadata | emd-27142.cif.gz | 6.9 KB | ||
Others | emd_27142_half_map_1.map.gz emd_27142_half_map_2.map.gz | 84.2 MB 84.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27142 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27142 | HTTPS FTP |
-Related structure data
Related structure data | 8d2lMC 8d2kC 8d2nC 8d2oC 8d2pC 8d2qC C: citing same article (ref.) M: atomic model generated by this map |
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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_27142.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | AcCas9 Cleavage intermediate 1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Halfmap1
File | emd_27142_half_map_1.map | ||||||||||||
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Annotation | Halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap2
File | emd_27142_half_map_2.map | ||||||||||||
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Annotation | Halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CryoEM Structure of AceCas9 (Cleavage intermediate 1)
+Supramolecule #1: CryoEM Structure of AceCas9 (Cleavage intermediate 1)
+Supramolecule #2: CRISPR-associated endonuclease, Csn1 family/RNA
+Supramolecule #3: DNA
+Macromolecule #1: CRISPR-associated endonuclease, Csn1 family
+Macromolecule #2: Single guide RNA (106-MER)
+Macromolecule #3: DNA target strand (5'-D(*AP*GP*CP*TP*TP*GP*GP*TP*GP*TP*AP*TP*A)-3')
+Macromolecule #4: DNA target strand (5'-D(P*CP*CP*AP*GP*GP*AP*TP*CP*TP*TP*GP*CP*CP*...
+Macromolecule #5: DNA non-target strand (5'-D(P*TP*AP*TP*AP*CP*AP*CP*CP*AP*AP*GP*CP...
+Macromolecule #6: DNA non-target strand (5'-D(P*AP*GP*A)-3')
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: water
-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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196600 |