6XL1

crystal structure of cA4-activated Card1(D294N)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 10.1038/s41586-021-03206-x
  • Primary Citation of Related Structures:  
    6XL1, 6WXX, 6WXW, 6WXY

  • 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 ...

    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

    Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA. marraffini@rockefeller.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Card1 AB382Treponema succinifaciens DSM 2489Mutation(s): 1 
Gene Names: Tresu_2185
Find proteins for F2NWD3 (Treponema succinifaciens (strain ATCC 33096 / DSM 2489 / 6091))
Explore F2NWD3 
Go to UniProtKB:  F2NWD3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    cA4C4synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EPE
    Query on EPE

    Download Ideal Coordinates CCD File 
    B
    4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
    C8 H18 N2 O4 S
    JKMHFZQWWAIEOD-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    A, B
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.95 Å
    • R-Value Free: 0.202 
    • R-Value Work: 0.178 
    • R-Value Observed: 0.179 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 111.946α = 90
    b = 111.946β = 90
    c = 172.18γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PHENIXrefinement
    autoXDSdata reduction
    autoXDSdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    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