6WXY

crystal structure of cA6-bound Card1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

The Card1 nuclease provides defence during type III CRISPR immunity.

Rostol, J.T.Xie, W.Kuryavyi, V.Maguin, P.Kao, K.Froom, R.Patel, D.J.Marraffini, L.A.

(2021) Nature 590: 624-629

  • DOI: https://doi.org/10.1038/s41586-021-03206-x
  • Primary Citation of Related Structures:  
    6WXW, 6WXX, 6WXY, 6XL1

  • PubMed Abstract: 

    In the type III CRISPR-Cas immune response of prokaryotes, infection triggers the production of cyclic oligoadenylates that bind and activate proteins that contain a CARF domain 1,2 . Many type III loci are associated with proteins in which the CRISPR-associated Rossman fold (CARF) domain is fused to a restriction  endonuclease-like domain 3,4 . However, with the exception of the well-characterized Csm6 and Csx1 ribonucleases 5,6 , whether and how these inducible effectors provide defence is not known. Here we investigated a type III CRISPR accessory protein, which we name cyclic-oligoadenylate-activated single-stranded ribonuclease and single-stranded deoxyribonuclease 1 (Card1). Card1 forms a symmetrical dimer that has a large central cavity between its CRISPR-associated Rossmann fold and restriction endonuclease domains that binds cyclic tetra-adenylate. The binding of ligand results in a conformational change comprising the rotation of individual monomers relative to each other to form a more compact dimeric scaffold, in which a manganese cation coordinates the catalytic residues and activates the cleavage of single-stranded-but not double-stranded-nucleic acids (both DNA and RNA). In vivo, activation of Card1 induces dormancy of the infected hosts to provide immunity against phage infection and plasmids. Our results highlight the diversity of strategies used in CRISPR systems to provide immunity.


  • Organizational Affiliation

    Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Card1
B, C
382Treponema succinifaciens DSM 2489Mutation(s): 0 
Gene Names: Tresu_2185
UniProt
Find proteins for F2NWD3 (Treponema succinifaciens (strain ATCC 33096 / DSM 2489 / 6091))
Explore F2NWD3 
Go to UniProtKB:  F2NWD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2NWD3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
cA66synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.911α = 90
b = 124.763β = 96.79
c = 42.259γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references, Structure summary
  • Version 1.2: 2021-02-10
    Changes: Database references
  • Version 1.3: 2021-02-17
    Changes: Database references
  • Version 1.4: 2021-03-10
    Changes: Database references
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.6: 2024-04-03
    Changes: Refinement description