6MUU

Cryo-EM structure of Csm-crRNA binary complex in type III-A CRISPR-Cas system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity.

Jia, N.Mo, C.Y.Wang, C.Eng, E.T.Marraffini, L.A.Patel, D.J.

(2019) Mol Cell 73: 264

  • DOI: https://doi.org/10.1016/j.molcel.2018.11.007
  • Primary Citation of Related Structures:  
    6MUA, 6MUR, 6MUS, 6MUT, 6MUU

  • PubMed Abstract: 

    Type ΙΙΙ CRISPR-Cas systems provide robust immunity against foreign RNA and DNA by sequence-specific RNase and target RNA-activated sequence-nonspecific DNase and RNase activities. We report on cryo-EM structures of Thermococcus onnurineus Csm crRNA binary, Csm crRNA -target RNA and Csm crRNA -target RNA anti-tag ternary complexes in the 3.1 Å range. The topological features of the crRNA 5'-repeat tag explains the 5'-ruler mechanism for defining target cleavage sites, with accessibility of positions -2 to -5 within the 5'-repeat serving as sensors for avoidance of autoimmunity. The Csm3 thumb elements introduce periodic kinks in the crRNA-target RNA duplex, facilitating cleavage of the target RNA with 6-nt periodicity. Key Glu residues within a Csm1 loop segment of Csm crRNA adopt a proposed autoinhibitory conformation suggestive of DNase activity regulation. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into Csm crRNA complex assembly, mechanisms underlying RNA targeting and site-specific periodic cleavage, regulation of DNase cleavage activity, and autoimmunity suppression.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Southern University of Science and Technology, Shenzhen, Guangdong 518055, China. Electronic address: jian@mskcc.org.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Csm1791Thermococcus onnurineusMutation(s): 0 
UniProt
Find proteins for B6YWB8 (Thermococcus onnurineus (strain NA1))
Explore B6YWB8 
Go to UniProtKB:  B6YWB8
Entity Groups  
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UniProt GroupB6YWB8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Csm2187Thermococcus onnurineusMutation(s): 0 
UniProt
Find proteins for B6YWB9 (Thermococcus onnurineus (strain NA1))
Explore B6YWB9 
Go to UniProtKB:  B6YWB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YWB9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Csm3
C, D
291Thermococcus onnurineusMutation(s): 0 
UniProt
Find proteins for B6YWC0 (Thermococcus onnurineus (strain NA1))
Explore B6YWC0 
Go to UniProtKB:  B6YWC0
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UniProt GroupB6YWC0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Csm4289Thermococcus onnurineusMutation(s): 0 
UniProt
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
Explore B6YWC1 
Go to UniProtKB:  B6YWC1
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UniProt GroupB6YWC1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Csm5403Thermococcus onnurineusMutation(s): 0 
UniProt
Find proteins for B6YWC2 (Thermococcus onnurineus (strain NA1))
Explore B6YWC2 
Go to UniProtKB:  B6YWC2
Entity Groups  
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UniProt GroupB6YWC2
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (25-MER)38Thermococcus onnurineus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references