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- PDB-6r7b: Crystal structure of Csx1 in complex with cyclic oligoadenylate c... -
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Basic information
Entry | Database: PDB / ID: 6r7b | ||||||
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Title | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 1 | ||||||
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Function / homology | CRISPR system endoribonuclease Csx1-like / CRISPR system endoribonuclease Csx1, HEPN domain / ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Molina, R. / Montoya, G. / Sofos, N. / Stella, S. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 559.2 KB | Display | ![]() |
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PDB format | ![]() | 470.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4691C ![]() 6qzqC ![]() 6qztSC ![]() 6r9rC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51859.395 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Although Chain D and E have the same composition, due to crystal symmetry chain E is just a half of D. Then chain D contains 4 adenosine monophosphate while chain E contains 2 adenosine monophosphates Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.85 % / Description: PLATES |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M TRICINE PH=8.0, 0.35M NACL, 28% PEG1000, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.12→178.63 Å / Num. obs: 24510 / % possible obs: 93 % / Redundancy: 11.6 % / Biso Wilson estimate: 115.32 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.12→3.46 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1226 / CC1/2: 0.57 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6QZT Resolution: 3.12→48.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.556
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Displacement parameters | Biso mean: 131.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.12→48.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.12→3.33 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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