+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14245 | ||||||||||||
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Title | elongated Cascade complex from type I-A CRISPR-Cas system | ||||||||||||
Map data | partial | ||||||||||||
Sample |
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Keywords | elongated Cascade complex / cascade / type I-A / genome editing / ANTIVIRAL PROTEIN | ||||||||||||
Function / homology | Function and homology information exonuclease activity / endonuclease activity / defense response to virus / nucleic acid binding / RNA helicase activity / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) / Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Hu C / Ni D / Nam KH / Terns M / Stahlberg H / Ke A | ||||||||||||
Funding support | United States, Switzerland, 3 items
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Citation | Journal: To Be Published Title: Structural snapshots for an atypic type I CRISPR-Cas system Authors: Ni D / Hu C / Nam KH / Terns M / Stahlberg H / Ke A | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14245.map.gz | 63.1 MB | EMDB map data format | |
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Header (meta data) | emd-14245-v30.xml emd-14245.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14245_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_14245.png | 107.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14245 | HTTPS FTP |
-Validation report
Summary document | emd_14245_validation.pdf.gz | 584.9 KB | Display | EMDB validaton report |
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Full document | emd_14245_full_validation.pdf.gz | 584.4 KB | Display | |
Data in XML | emd_14245_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_14245_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14245 | HTTPS FTP |
-Related structure data
Related structure data | 7r2kMC 7r21C 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_14245.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | partial | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.3325 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : elongated Cascade complex from Pyrococcus furiosus type I-A CRISP...
+Supramolecule #1: elongated Cascade complex from Pyrococcus furiosus type I-A CRISP...
+Macromolecule #1: CRISPR-associated helicase Cas3
+Macromolecule #2: Cas11a
+Macromolecule #4: Cas7a
+Macromolecule #5: CRISPR-associated endonuclease Cas3-HD
+Macromolecule #6: Type I-A CRISPR-associated protein Cas5
+Macromolecule #9: Cas8
+Macromolecule #3: DNA (5'-D(P*TP*AP*CP*AP*AP*GP*GP*GP*A)-3')
+Macromolecule #8: DNA (5'-D(P*TP*CP*CP*C)-3')
+Macromolecule #7: crRNA (57-MER)
+Macromolecule #10: NICKEL (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride |
Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 4s force 0. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 8500 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7r2k: |