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Yorodumi- EMDB-17702: Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17702 | |||||||||
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Title | Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system | |||||||||
Map data | Map sharpened using phenix.auto_sharpen_1.21rc1-4903 using _iso_to_d_cut procedure and 3.24A cutoff. | |||||||||
Sample |
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Keywords | Cas9 / CRISPR-Cas / PAM / spacer acquisition / RNA BINDING 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 | Streptococcus thermophilus DGCC 7710 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | |||||||||
Authors | Sasnauskas G / Gaizauskaite U / Tamulaitiene G | |||||||||
Funding support | Lithuania, 1 items
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Citation | Journal: To Be Published Title: Structural basis for spacer acquisition in a type II-A CRISPR-Cas system Authors: Sasnauskas G / Gaizauskaite U / Tamulaitiene G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17702.map.gz | 27.1 MB | EMDB map data format | |
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Header (meta data) | emd-17702-v30.xml emd-17702.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17702_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_17702.png | 157.1 KB | ||
Masks | emd_17702_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-17702.cif.gz | 7.3 KB | ||
Others | emd_17702_additional_1.map.gz emd_17702_half_map_1.map.gz emd_17702_half_map_2.map.gz | 15.3 MB 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17702 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17702 | HTTPS FTP |
-Validation report
Summary document | emd_17702_validation.pdf.gz | 882.2 KB | Display | EMDB validaton report |
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Full document | emd_17702_full_validation.pdf.gz | 881.8 KB | Display | |
Data in XML | emd_17702_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_17702_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17702 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17702 | HTTPS FTP |
-Related structure data
Related structure data | 8pj9MC 8pk1C 8q2nC 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_17702.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Map sharpened using phenix.auto_sharpen_1.21rc1-4903 using _iso_to_d_cut procedure and 3.24A cutoff. | ||||||||||||||||||||||||||||||||||||
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_17702_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_17702_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17702_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17702_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
+Supramolecule #1: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
+Supramolecule #2: CRISPR-associated endonuclease Cas9
+Supramolecule #3: crRNA, chain B and tracrRNA, chain C
+Supramolecule #4: DNA oligoduplex, target strand, chains D,E and DNA oligoduplex, n...
+Macromolecule #1: CRISPR-associated endonuclease Cas9
+Macromolecule #2: crRNA, chain B
+Macromolecule #3: tracrRNA, chain C
+Macromolecule #4: DNA oligoduplex, target strand, chains D,E
+Macromolecule #5: DNA oligoduplex, non-target strand, chain F
+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: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1744 / Average exposure time: 46.33 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000 |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8pj9: |