6MUT

Cryo-EM structure of ternary Csm-crRNA-target RNA with anti-tag sequence complex in type III-A CRISPR-Cas system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: 10.1016/j.molcel.2018.11.007
  • Primary Citation of Related Structures:  
    6MUS, 6MUR, 6MUU, 6MUT, 6MUA

  • 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 ...

    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: pateld@mskcc.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Csm1A791Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0893
EC: 3.1 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for B6YWB8 (Thermococcus onnurineus (strain NA1))
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Go to UniProtKB:  B6YWB8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Csm2B187Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0894
UniProt
Find proteins for B6YWB9 (Thermococcus onnurineus (strain NA1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Csm3C, D291Thermococcus onnurineusMutation(s): 1 
Gene Names: TON_0895
UniProt
Find proteins for B6YWC0 (Thermococcus onnurineus (strain NA1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Csm4E289Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0896
UniProt
Find proteins for B6YWC1 (Thermococcus onnurineus (strain NA1))
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein Csm5H [auth F]403Thermococcus onnurineusMutation(s): 0 
Gene Names: TON_0897
UniProt
Find proteins for B6YWC2 (Thermococcus onnurineus (strain NA1))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*GP*CP*GP*GP*GP*CP*AP*GP*AP*GP*GP*C)-3')F [auth G]38Thermococcus onnurineus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*CP*UP*CP*UP*GP*CP*CP*CP*GP*CP*CP*UP*UP*UP*CP*CP*AP*C)-3')G [auth H]45Thermococcus onnurineus
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A], J [auth C], K [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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