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Yorodumi- PDB-9c68: The CRISPR associated CARF-adenosine deaminase Cad1-CARF in the c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c68 | ||||||
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Title | The CRISPR associated CARF-adenosine deaminase Cad1-CARF in the cA6 bound form | ||||||
Components |
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Keywords | Antiviral Protein/RNA / Type-III CRISPR defense system / CARF-effector protein / adaptive immunity / deamination defense strategy / cyclic Hexa-adenylate / Antiviral Protein-RNA complex | ||||||
Function / homology | Function and homology information inosine biosynthetic process / adenosine catabolic process / adenosine deaminase activity Similarity search - Function | ||||||
Biological species | Bacteroidales bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Majumder, P. / Patel, D.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2024 Title: The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity. Authors: Christian F Baca / Puja Majumder / James H Hickling / Linzhi Ye / Marianna Teplova / Sean F Brady / Dinshaw J Patel / Luciano A Marraffini / Abstract: Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA) molecules that activate effector proteins that contain CRISPR-associated ...Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA) molecules that activate effector proteins that contain CRISPR-associated Rossman fold (CARF) domains. Here, we characterized the function and structure of an effector in which the CARF domain is fused to an adenosine deaminase domain, CRISPR-associated adenosine deaminase 1 (Cad1). We show that upon binding of cA or cA to its CARF domain, Cad1 converts ATP to ITP, both in vivo and in vitro. Cryoelectron microscopy (cryo-EM) structural studies on full-length Cad1 reveal an hexameric assembly composed of a trimer of dimers, with bound ATP at inter-domain sites required for activity and ATP/ITP within deaminase active sites. Upon synthesis of cA during phage infection, Cad1 activation leads to a growth arrest of the host that prevents viral propagation. Our findings reveal that CRISPR-Cas systems employ a wide range of molecular mechanisms beyond nucleic acid degradation to provide adaptive immunity in prokaryotes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c68.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c68.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 9c68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c68_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 9c68_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 9c68_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 9c68_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/9c68 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/9c68 | HTTPS FTP |
-Related structure data
Related structure data | 9c67C 9c69C 9c6aC 9c6cC 9c6fC 9c77C 9cdbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21069.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroidales bacterium (bacteria) / Gene: DCM62_02910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3C0QUR5 #2: RNA chain | | Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacteroidales bacterium (bacteria) #3: Water | ChemComp-HOH / | Has protein modification | N | |
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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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: small diamond |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M sodium acetate pH 4.5, 35 % (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 4, 2024 / Details: KB bimorph mirrors |
Radiation | Monochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→74.41 Å / Num. obs: 37752 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.038 / Rrim(I) all: 0.053 / Χ2: 0.92 / Net I/σ(I): 9.5 / Num. measured all: 69781 |
Reflection shell | Resolution: 1.82→1.86 Å / % possible obs: 99.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 2.017 / Num. measured all: 4137 / Num. unique obs: 2181 / CC1/2: 0.421 / Rpim(I) all: 2.017 / Rrim(I) all: 2.853 / Χ2: 0.79 / Net I/σ(I) obs: 0.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→42.96 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 34.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→42.96 Å
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Refine LS restraints |
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LS refinement shell |
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