5B2T

Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA and target DNA (TGCG PAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9

Hirano, S.Nishimasu, H.Ishitani, R.Nureki, O.

(2016) Mol Cell 61: 886-894

  • DOI: 10.1016/j.molcel.2016.02.018
  • Primary Citation of Related Structures:  
    5B2R, 5B2T, 5B2S

  • PubMed Abstract: 
  • The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets bearing a PAM (protospacer adjacent motif) and complementarity to the guide RNA. A recent study showed that, whereas wild-type Streptococcus pyogenes Cas9 (SpCas9) recognizes the 5' ...

    The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets bearing a PAM (protospacer adjacent motif) and complementarity to the guide RNA. A recent study showed that, whereas wild-type Streptococcus pyogenes Cas9 (SpCas9) recognizes the 5'-NGG-3' PAM, the engineered VQR, EQR, and VRER SpCas9 variants recognize the 5'-NGA-3', 5'-NGAG-3', and 5'-NGCG-3' PAMs, respectively, thus expanding the targetable sequences in Cas9-mediated genome editing applications. Here, we present the high-resolution crystal structures of the three SpCas9 variants in complexes with a single-guide RNA and its altered PAM-containing, partially double-stranded DNA targets. A structural comparison of the three SpCas9 variants with wild-type SpCas9 revealed that the multiple mutations synergistically induce an unexpected displacement in the phosphodiester backbone of the PAM duplex, thereby allowing the SpCas9 variants to directly recognize the altered PAM nucleotides. Our findings explain the altered PAM specificities of the SpCas9 variants and establish a framework for further rational engineering of CRISPR-Cas9.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: nureki@bs.s.u-tokyo.ac.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9B1372Streptococcus pyogenes serotype M1Mutation(s): 8 
Gene Names: cas9csn1SPy_1046
EC: 3.1
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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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Guide RNAA81Streptococcus pyogenes
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
Target DNAC28Streptococcus pyogenes
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    Non-target DNA, DNA (5'-D(*TP*GP*CP*GP*AP*TP*TP*G)-3')D8Streptococcus pyogenes
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

    Download CCD File 
    A, B
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    ACT
    Query on ACT

    Download CCD File 
    A
    ACETATE ION
    C2 H3 O2
    QTBSBXVTEAMEQO-UHFFFAOYSA-M
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    A, B
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.223 
    • R-Value Work: 0.204 
    • R-Value Observed: 0.205 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 176.967α = 90
    b = 69.448β = 109.67
    c = 188.199γ = 90
    Software Package:
    Software NamePurpose
    Aimlessdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2016-03-23
      Type: Initial release
    • Version 1.1: 2016-04-06
      Changes: Database references
    • Version 1.2: 2017-10-04
      Changes: Data collection, Database references, Derived calculations