9KJ6 | pdb_00009kj6

Crystal Structure of SpCas9 ternary complex, amino acids (1242-1263) replaced with Gly-Ser linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 
    0.271 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural and functional insights into internal domain replacement in SpCas9 for protein engineering.

Kim, S.Won, H.Bae, J.Kim, J.Choi, J.Richar, H.Kim, Y.G.Choi, H.J.

(2025) Sci Rep 15: 41528-41528

  • DOI: https://doi.org/10.1038/s41598-025-25367-9
  • Primary Citation Related Structures: 
    9KJ6

  • PubMed Abstract: 

    The CRISPR-Cas9 system has emerged as a powerful tool for precise genome editing, with ongoing research focused on enhancing its reliability and expanding its versatility. One effective strategy involves the integration of foreign functional domains into Cas9 to confer new capabilities. However, successful integration requires identification of insertion sites that preserve the protein's structural integrity and function. In this study, we identified a C-terminal region of Streptococcus pyogenes Cas9 (SpCas9), spanning residues 1242-1263, as a viable site for domain replacement. Structural and biochemical analyses of a SpCas9 variant lacking this region confirmed its dispensability for SpCas9 activity. As a proof of concept, we substituted this segment with the evolved E. coli tRNA adenosine deaminase (TadA), a key component of adenine base editors. Functional evaluation of this engineered SpCas9-TadA variant demonstrated deamination efficiency comparable to that of the ABE8e, with the potential to modulate the editing window through linker design. These results highlight the potential of targeted engineering of this region to develop more precise and versatile genome editing tools.


  • Organizational Affiliation
    • Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 211.17 kDa 
  • Atom Count: 13,121 
  • Modeled Residue Count: 1,479 
  • Deposited Residue Count: 1,529 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9/Csn11,357Streptococcus pyogenesMutation(s): 2 
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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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
single-guide RNA102Streptococcus pyogenes
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Target Strand of double-stranded DNA43synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Non-target Strand of double-stranded DNA27synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free:  0.271 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.55α = 90
b = 146.85β = 90
c = 222.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Samsung Science and Technology FoundationKorea, Republic OfSRFC-MA1801-09

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references