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- EMDB-0442: Type III-A CRISPR Effector Subcomplex from Staphylococcus epiderm... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0442 | |||||||||
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Title | Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a | |||||||||
![]() | Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a, primary map | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
![]() | Dorsey BW / Mondragon A | |||||||||
![]() | ![]() Title: Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM. Authors: Bryan W Dorsey / Lei Huang / Alfonso Mondragón / ![]() Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas ...Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and types. Class 1 CRISPR-Cas systems form multi-protein effector complexes that includes a guide RNA (crRNA) used to identify the target for destruction. Here we present crystal structures of Staphylococcus epidermidis Type III-A CRISPR subunits Csm2 and Csm3 and a 5.2 Å resolution single-particle cryo-electron microscopy (cryo-EM) reconstruction of an in vivo assembled effector subcomplex including the crRNA. The structures help to clarify the quaternary architecture of Type III-A effector complexes, and provide details on crRNA binding, target RNA binding and cleavage, and intermolecular interactions essential for effector complex assembly. The structures allow a better understanding of the organization of Type III-A CRISPR effector complexes as well as highlighting the overall similarities and differences with other Class 1 effector complexes. | |||||||||
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 | ![]() | 51.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.8 KB | Display | ![]() |
Images | ![]() | 64.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.7 KB | Display | ![]() |
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Full document | ![]() | 77.8 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Type III-A CRISPR Effector Subcomplex from Staphylococcus epiderm...
Entire | Name: Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a |
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Components |
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-Supramolecule #1: Type III-A CRISPR Effector Subcomplex from Staphylococcus epiderm...
Supramolecule | Name: Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 255 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.20 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Details: Glow discharged with 15mA. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 4 seconds with +5 force before plunging.. |
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Electron microscopy
Microscope | JEOL 3200FS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 7 / Number real images: 1037 / Average exposure time: 8.0 sec. / Average electron dose: 37.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 40323 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |