8T6O

SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 0 bp R-loop


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9.

Hibshman, G.N.Bravo, J.P.K.Hooper, M.M.Dangerfield, T.L.Zhang, H.Finkelstein, I.J.Johnson, K.A.Taylor, D.W.

(2024) Nat Commun 15: 3663-3663

  • DOI: https://doi.org/10.1038/s41467-024-47830-3
  • Primary Citation of Related Structures:  
    8SPQ, 8SQH, 8SRS, 8T6O, 8T6P, 8T6S, 8T6T, 8T6X, 8T6Y, 8T76, 8T77, 8T78, 8T79, 8T7S, 8TZZ, 8U3Y

  • PubMed Abstract: 

    CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.


  • Organizational Affiliation

    Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9/Csn1B [auth A]1,369Streptococcus pyogenesMutation(s): 11 
Gene Names: cas9csn1SPy_1046
EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Explore Q99ZW2 
Go to UniProtKB:  Q99ZW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99ZW2
Sequence Annotations
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Entity ID: 1
MoleculeChains LengthOrganismImage
NTSA [auth D]55Escherichia phage Lambda
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
gRNAC [auth B]87Streptococcus pyogenes
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
TSD [auth C]55Escherichia phage Lambda
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesF-1938
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138348

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references