6AI6

Crystal structure of SpCas9-NG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Engineered CRISPR-Cas9 nuclease with expanded targeting space

Nishimasu, H.Shi, X.Ishiguro, S.Gao, L.Hirano, S.Okazaki, S.Noda, T.Abudayyeh, O.O.Gootenberg, J.S.Mori, H.Oura, S.Holmes, B.Tanaka, M.Seki, M.Hirano, H.Aburatani, H.Ishitani, R.Ikawa, M.Yachie, N.Zhang, F.Nureki, O.

(2018) Science 361: 1259-1262

  • DOI: 10.1126/science.aas9129
  • Primary Citation of Related Structures:  
    6AI6

  • PubMed Abstract: 
  • The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Streptococcus pyogenes Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci ...

    The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Streptococcus pyogenes Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs. The crystal structure revealed that the loss of the base-specific interaction with the third nucleobase is compensated by newly introduced non-base-specific interactions, thereby enabling the NG PAM recognition. We showed that SpCas9-NG induces indels at endogenous target sites bearing NG PAMs in human cells. Furthermore, we found that the fusion of SpCas9-NG and the activation-induced cytidine deaminase (AID) mediates the C-to-T conversion at target sites with NG PAMs in human cells.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9/Csn1A1372Streptococcus pyogenes serotype M1Mutation(s): 8 
Gene Names: cas9csn1SPy_1046
EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Explore Q99ZW2 
Go to UniProtKB:  Q99ZW2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (81-MER)B81Streptococcus pyogenes
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (28-MER)C28Streptococcus pyogenes
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (8-MER)D8Streptococcus pyogenes
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    N [auth A], O [auth A], P [auth A]1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download Ideal Coordinates CCD File 
    E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
    E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  Q [auth A],  R [auth B]
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    M [auth A], S [auth B], T [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.243 
    • R-Value Work: 0.218 
    • R-Value Observed: 0.219 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 177.377α = 90
    b = 68.568β = 111.51
    c = 187.968γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    Aimlessdata scaling
    XDSdata reduction
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2018-10-31
      Type: Initial release