8S9X

CRISPR-Cas type III-D effector complex bound to self-target RNA in a post-cleavage state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

RNA targeting and cleavage by the type III-Dv CRISPR effector complex.

Schwartz, E.A.Bravo, J.P.K.Ahsan, M.Macias, L.A.McCafferty, C.L.Dangerfield, T.L.Walker, J.N.Brodbelt, J.S.Palermo, G.Fineran, P.C.Fagerlund, R.D.Taylor, D.W.

(2024) Nat Commun 15: 3324-3324

  • DOI: https://doi.org/10.1038/s41467-024-47506-y
  • Primary Citation of Related Structures:  
    8S9T, 8S9V, 8S9X

  • PubMed Abstract: 

    CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction 1-5 . Target RNA cleavage at regular intervals is characteristic of type III effector complexes 6-8 . Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors 9,10 , in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2'-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.


  • Organizational Affiliation

    Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas7-Cas5-Cas11791Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: sll7066
UniProt
Find proteins for Q6ZED2 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Go to UniProtKB:  Q6ZED2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZED2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TIGR03984 family CRISPR-associated protein193Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: sll7064
UniProt
Find proteins for Q6ZED4 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q6ZED4 
Go to UniProtKB:  Q6ZED4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZED4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cas10575Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: sll7067
UniProt
Find proteins for Q6ZED1 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q6ZED1 
Go to UniProtKB:  Q6ZED1
Entity Groups  
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UniProt GroupQ6ZED1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cas7-2x522Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: sll7065
UniProt
Find proteins for Q6ZED3 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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UniProt GroupQ6ZED3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TIGR03986 family CRISPR-associated RAMP protein795Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: sll7063
UniProt
Find proteins for Q6ZED5 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q6ZED5 
Go to UniProtKB:  Q6ZED5
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UniProt GroupQ6ZED5
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Entity ID: 6
MoleculeChains LengthOrganismImage
CRISPR RNA37Synechocystis sp. PCC 6803
Sequence Annotations
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Entity ID: 7
MoleculeChains LengthOrganismImage
Self-target RNA60Synechocystis sp. PCC 6803
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138348

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references