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Yorodumi- PDB-6nbt: CRISPR Complex Subunit Csm3 from Staphylococcus epidermidis RP62a -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nbt | ||||||
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Title | CRISPR Complex Subunit Csm3 from Staphylococcus epidermidis RP62a | ||||||
Components | CRISPR-associated protein | ||||||
Keywords | RNA BINDING PROTEIN / CRISPR / RNA Binding / RNA Recognition Motif / Samarium (III) chloride | ||||||
Function / homology | CRISPR-associated RAMP Csm3 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / endonuclease activity / RNA binding / SAMARIUM (III) ION / CRISPR system Cms endoribonuclease Csm3 Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Dorsey, B.W. / Mondragon, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2019 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nbt.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nbt.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/6nbt ftp://data.pdbj.org/pub/pdb/validation_reports/nb/6nbt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 27012.383 Da / Num. of mol.: 2 / Fragment: Subunit Csm3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (bacteria) Strain: ATCC 35984 / RP62A / Cell line: 35984D-5 / Gene: SERP2459 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q5HK91 #2: Chemical | #3: Chemical | ChemComp-SM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, calcium acetate, 2-(N-morpholino)ethanesulfonic acid (MES) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 28, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.57 Å / Num. obs: 16891 / % possible obs: 98.2 % / Redundancy: 6.8 % / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.4→2.49 Å |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.897 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.284 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.19 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→25 Å
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Refine LS restraints |
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