+Open data
-Basic information
Entry | Database: PDB / ID: 6ifn | |||||||||
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Title | Crystal structure of Type III-A CRISPR Csm complex | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN / Csm complex / Type III-A / CRISPR-Cas system | |||||||||
Function / homology | Function and homology information exonuclease activity / transferase activity / endonuclease activity / defense response to virus / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Streptococcus thermophilus ND03 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | You, L. / Wang, J. / Wang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell / Year: 2019 Title: Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference. Authors: Lilan You / Jun Ma / Jiuyu Wang / Daria Artamonova / Min Wang / Liang Liu / Hua Xiang / Konstantin Severinov / Xinzheng Zhang / Yanli Wang / Abstract: Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, ...Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5' tag of crRNA, the 3' anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ifn.cif.gz | 466.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ifn.ent.gz | 369.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ifn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/6ifn ftp://data.pdbj.org/pub/pdb/validation_reports/if/6ifn | HTTPS FTP |
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-Related structure data
Related structure data | 9653C 9654C 9655C 9656C 9657C 9658C 9659C 9660C 6ifkC 6iflSC 6ifrC 6ifuC 6ifyC 6ifzC 6ig0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Type III-A CRISPR-associated protein ... , 2 types, 3 molecules ACD
#1: Protein | Mass: 86977.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U2M0F3 |
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#4: Protein | Mass: 14848.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Gene: csm2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U2M049 |
-Type III-A CRISPR-associated RAMP protein ... , 3 types, 5 molecules FEGBH
#2: Protein | Mass: 24585.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Gene: csm3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U2M035 #3: Protein | | Mass: 33828.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Gene: csm4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U2M037 #5: Protein | | Mass: 41102.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Gene: csm5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2U2M038 |
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-RNA chain , 1 types, 1 molecules N
#6: RNA chain | Mass: 12638.505 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus ND03 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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-Non-polymers , 2 types, 2 molecules
#7: Chemical | ChemComp-ZN / |
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#8: Chemical | ChemComp-MN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 20% w/v polyethylene glycol 20,000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 70612 / % possible obs: 97.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.446 / Num. unique obs: 6836 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IFL Resolution: 2.9→48.68 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.006 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / 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: 51.084 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→48.68 Å
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Refine LS restraints |
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