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Open data
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Basic information
Entry | Database: PDB / ID: 6ifl | ||||||
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Title | Cryo-EM structure of type III-A Csm-NTR complex | ||||||
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![]() | RNA BINDING PROTEIN / Csm complex / Type III-A / CRISPR-Cas system | ||||||
Function / homology | ![]() exonuclease activity / transferase activity / endonuclease activity / defense response to virus / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||
![]() | You, L. / Ma, J. / Wang, J. / Zhang, X. / Wang, Y. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426.9 KB | Display | ![]() |
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PDB format | ![]() | 339 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1019.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 61.4 KB | Display | |
Data in CIF | ![]() | 96 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9654MC ![]() 9653C ![]() 9655C ![]() 9656C ![]() 9657C ![]() 9658C ![]() 9659C ![]() 9660C ![]() 6ifkC ![]() 6ifnC ![]() 6ifrC ![]() 6ifuC ![]() 6ifyC ![]() 6ifzC ![]() 6ig0C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Type III-A CRISPR-associated protein ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 86976.734 Da / Num. of mol.: 1 / Mutation: D16N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cas10 / Production host: ![]() ![]() |
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#2: Protein | Mass: 14848.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: csm2 / Production host: ![]() ![]() |
-Type III-A CRISPR-associated RAMP protein ... , 3 types, 5 molecules DEFGH
#3: Protein | Mass: 24584.855 Da / Num. of mol.: 3 / Mutation: D33N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: csm3 / Production host: ![]() ![]() #4: Protein | | Mass: 33828.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: csm4 / Production host: ![]() ![]() #5: Protein | | Mass: 41102.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-RNA chain , 2 types, 2 molecules IJ
#6: RNA chain | Mass: 11392.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#7: RNA chain | Mass: 13937.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.5 | |||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 60 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133127 / Symmetry type: POINT |