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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7347 | |||||||||
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Title | CRISPR RNA-guided surveillance complex, pre-nicking | |||||||||
![]() | CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state | |||||||||
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![]() | CRISPR-Cas / Cascade / Cas3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | ![]() nuclease activity / maintenance of CRISPR repeat elements / defense response to virus / RNA helicase activity / RNA binding / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
![]() | Xiao Y / Luo M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure basis for RNA-guided DNA degradation by Cascade and Cas3. Authors: Yibei Xiao / Min Luo / Adam E Dolan / Maofu Liao / Ailong Ke / ![]() Abstract: Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and ...Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and the nuclease-helicase fusion enzyme Cas3, respectively. Here, we present a 3.7-angstrom-resolution cryo-electron microscopy (cryo-EM) structure of the Type I-E Cascade/R-loop/Cas3 complex, poised to initiate DNA degradation. Cas3 distinguishes Cascade conformations and only captures the R-loop-forming Cascade, to avoid cleaving partially complementary targets. Its nuclease domain recruits the nontarget strand (NTS) DNA at a bulged region for the nicking of single-stranded DNA. An additional 4.7-angstrom-resolution cryo-EM structure captures the postnicking state, in which the severed NTS retracts to the helicase entrance, to be threaded for adenosine 5'-triphosphate-dependent processive degradation. These snapshots form the basis for understanding RNA-guided DNA degradation in Type I-E CRISPR-Cas systems. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.2 KB 23.2 KB | Display Display | ![]() |
Images | ![]() | 109.4 KB | ||
Filedesc metadata | ![]() | 7.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 635.8 KB | Display | ![]() |
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Full document | ![]() | 635.4 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c66MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CRISPR RNA-guided surveillance complex with Cas3 bound in its pre-nicking state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : CRISPR RNA-guided surveillance complex with Cas3 bound in its pre...
+Supramolecule #1: CRISPR RNA-guided surveillance complex with Cas3 bound in its pre...
+Macromolecule #1: CRISPR-associated helicase, Cas3 family
+Macromolecule #2: CRISPR-associated protein, Cse1 family
+Macromolecule #3: CRISPR-associated protein, Cse4 family
+Macromolecule #4: Uncharacterized protein
+Macromolecule #7: CRISPR-associated protein, Cas5e family
+Macromolecule #9: CRISPR-associated protein, Cse3 family
+Macromolecule #5: crRNA
+Macromolecule #6: Target strand
+Macromolecule #8: Nontarget strand
+Macromolecule #10: FE (III) ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM HEPES pH 7.5, 150 mM NaCl, 5 mM DTT |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80.0 K / Max: 105.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1428 / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | ![]() PDB-6c66: |