+Open data
-Basic information
Entry | Database: PDB / ID: 5xwp | ||||||
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Title | Crystal structure of LbuCas13a-crRNA-target RNA ternary complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / LbuCas13a / C2c2 / crRNA / target RNA / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | : / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a Function and homology information | ||||||
Biological species | Leptotrichia buccalis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.086 Å | ||||||
Authors | Liu, L. / Li, X. / Li, Z. / Wang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2017 Title: The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a. Authors: Liang Liu / Xueyan Li / Jun Ma / Zongqiang Li / Lilan You / Jiuyu Wang / Min Wang / Xinzheng Zhang / Yanli Wang / Abstract: Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a ...Cas13a, a type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, degrades invasive RNAs targeted by CRISPR RNA (crRNA) and has potential applications in RNA technology. To understand how Cas13a is activated to cleave RNA, we have determined the crystal structure of Leptotrichia buccalis (Lbu) Cas13a bound to crRNA and its target RNA, as well as the cryo-EM structure of the LbuCas13a-crRNA complex. The crRNA-target RNA duplex binds in a positively charged central channel of the nuclease (NUC) lobe, and Cas13a protein and crRNA undergo a significant conformational change upon target RNA binding. The guide-target RNA duplex formation triggers HEPN1 domain to move toward HEPN2 domain, activating the HEPN catalytic site of Cas13a protein, which subsequently cleaves both single-stranded target and collateral RNAs in a non-specific manner. These findings reveal how Cas13a of type VI CRISPR-Cas systems defend against RNA phages and set the stage for its development as a tool for RNA manipulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xwp.cif.gz | 551.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xwp.ent.gz | 451.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xwp_validation.pdf.gz | 504.4 KB | Display | wwPDB validaton report |
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Full document | 5xwp_full_validation.pdf.gz | 660.3 KB | Display | |
Data in XML | 5xwp_validation.xml.gz | 97.1 KB | Display | |
Data in CIF | 5xwp_validation.cif.gz | 133.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/5xwp ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xwp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 139627.047 Da / Num. of mol.: 2 / Mutation: R1048A, H1053A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptotrichia buccalis (bacteria) Strain: ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b Gene: Lebu_1799 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: C7NBY4 #2: RNA chain | Mass: 18869.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: RNA chain | Mass: 9680.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.1 M L-Proline, 8% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→50 Å / Num. obs: 61255 / % possible obs: 98.6 % / Redundancy: 15 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 14 |
Reflection shell | Resolution: 3.08→3.13 Å / Redundancy: 10 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 3.5 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.086→48.179 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 22.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.086→48.179 Å
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Refine LS restraints |
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LS refinement shell |
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