6JOO

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9.

Hirano, S.Abudayyeh, O.O.Gootenberg, J.S.Horii, T.Ishitani, R.Hatada, I.Zhang, F.Nishimasu, H.Nureki, O.

(2019) Nat Commun 10: 1968-1968

  • DOI: 10.1038/s41467-019-09741-6
  • Primary Citation of Related Structures:  
    6JOO

  • PubMed Abstract: 
  • The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets bearing a protospacer adjacent motif (PAM) and complementarity to an RNA guide. Unlike other Cas9 orthologs, Corynebacterium diphtheriae Cas9 (CdCas9) recognizes the promiscuous ...

    The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets bearing a protospacer adjacent motif (PAM) and complementarity to an RNA guide. Unlike other Cas9 orthologs, Corynebacterium diphtheriae Cas9 (CdCas9) recognizes the promiscuous NNRHHHY PAM. However, the CdCas9-mediated PAM recognition mechanism remains unknown. Here, we report the crystal structure of CdCas9 in complex with the guide RNA and its target DNA at 2.9 Å resolution. The structure reveals that CdCas9 recognizes the NNRHHHY PAM via a combination of van der Waals interactions and base-specific hydrogen bonds. Moreover, we find that CdCas9 exhibits robust DNA cleavage activity with the optimal 22-nucleotide length guide RNAs. Our findings highlight the mechanistic diversity of the PAM recognition by Cas9 orthologs, and provide a basis for the further engineering of the CRISPR-Cas9 genome-editor nucleases.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. nureki@bs.s.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein,CRISPR-associated endonuclease Cas9A927Corynebacterium diphtheriaeCorynebacterium diphtheriae NCTC 13129
This entity is chimeric
Mutation(s): 0 
Gene Names: cas9
EC: 3.1
Find proteins for Q6NKI3 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NKI3 
Go to UniProtKB:  Q6NKI3
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Guide RNAB113Corynebacterium diphtheriae
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Non-Target DNAD8Corynebacterium diphtheriae
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    (by identity cutoff)  |  Structure
    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    Target DNAC28Corynebacterium diphtheriae
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    EDO
    Query on EDO

    Download CCD File 
    A, B
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MSE
    Query on MSE
    AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.222 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 139.015α = 90
    b = 118.999β = 113.59
    c = 116.272γ = 90
    Software Package:
    Software NamePurpose
    Aimlessdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    DIALSdata reduction
    AutoSolphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2019-04-17
      Type: Initial release
    • Version 1.1: 2019-05-15
      Changes: Data collection, Database references