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Yorodumi- PDB-6r9r: Crystal structure of Csx1 in complex with cyclic oligoadenylate c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r9r | ||||||
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Title | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / CRISPR ASSOCIATED PROTEIN CARF HEPN RNAse | ||||||
Function / homology | : / CRISPR system endoribonuclease Csx1, CARF domain / RNA / CRISPR-associated (Cas) DxTHG family Function and homology information | ||||||
Biological species | Sulfolobus islandicus REY15A (acidophilic) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Molina, R. / Montoya, G. / Sofos, N. / Stella, S. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structure of Csx1-cOA complex reveals the basis of RNA decay in Type III-B CRISPR-Cas. Authors: Rafael Molina / Stefano Stella / Mingxia Feng / Nicholas Sofos / Vykintas Jauniskis / Irina Pozdnyakova / Blanca López-Méndez / Qunxin She / Guillermo Montoya / Abstract: Type III CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA. These activities promote the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases from the ...Type III CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA. These activities promote the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases from the Csm/Csx families, triggering a massive RNA decay to provide immunity from genetic invaders. Here we present the structure of Sulfolobus islandicus (Sis) Csx1-cOA complex revealing the allosteric activation of its RNase activity. SisCsx1 is a hexamer built by a trimer of dimers. Each dimer forms a cOA binding site and a ssRNA catalytic pocket. cOA undergoes a conformational change upon binding in the second messenger binding site activating ssRNA degradation in the catalytic pockets. Activation is transmitted in an allosteric manner through an intermediate HTH domain, which joins the cOA and catalytic sites. The RNase functions in a sequential cooperative fashion, hydrolyzing phosphodiester bonds in 5'-C-C-3'. The degradation of cOA by Ring nucleases deactivates SisCsx1, suggesting that this enzyme could be employed in biotechnological applications. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r9r.cif.gz | 562.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r9r.ent.gz | 472.2 KB | Display | PDB format |
PDBx/mmJSON format | 6r9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r9r_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 6r9r_full_validation.pdf.gz | 511.2 KB | Display | |
Data in XML | 6r9r_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 6r9r_validation.cif.gz | 73.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/6r9r ftp://data.pdbj.org/pub/pdb/validation_reports/r9/6r9r | HTTPS FTP |
-Related structure data
Related structure data | 4691C 6qzqC 6qztSC 6r7bC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Although the sequence of chains D and E are the same, due to crystal symmetry, E chain just contains 2 adenosine monophophates instead 4 since the other two ones left are obtained by symmetry Source: (synth.) synthetic construct (others) #2: Protein | Mass: 51946.469 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / Gene: SiRe_0884 / Production host: Sulfolobus islandicus (acidophilic) / References: UniProt: F0NE21 #3: 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: 3.5 Å3/Da / Density % sol: 64.89 % / Description: Plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES PH=7.5, 20 MM LI2SO4, 30% PEG 600, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→78.62 Å / Num. obs: 44353 / % possible obs: 93.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 101.68 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.7→2.88 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 2218 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QZT Resolution: 2.7→52.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.334
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Displacement parameters | Biso mean: 108.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→52.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å / Total num. of bins used: 50
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Refinement TLS params. | T22: -0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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