8E2R

Crystal structure of TadAC-1.14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Improved cytosine base editors generated from TadA variants.

Lam, D.K.Feliciano, P.R.Arif, A.Bohnuud, T.Fernandez, T.P.Gehrke, J.M.Grayson, P.Lee, K.D.Ortega, M.A.Sawyer, C.Schwaegerle, N.D.Peraro, L.Young, L.Lee, S.J.Ciaramella, G.Gaudelli, N.M.

(2023) Nat Biotechnol 41: 686-697

  • DOI: https://doi.org/10.1038/s41587-022-01611-9
  • Primary Citation of Related Structures:  
    8E2P, 8E2Q, 8E2R, 8E2S

  • PubMed Abstract: 

    Cytosine base editors (CBEs) enable programmable genomic C·G-to-T·A transition mutations and typically comprise a modified CRISPR-Cas enzyme, a naturally occurring cytidine deaminase, and an inhibitor of uracil repair. Previous studies have shown that CBEs utilizing naturally occurring cytidine deaminases may cause unguided, genome-wide cytosine deamination. While improved CBEs that decrease stochastic genome-wide off-targets have subsequently been reported, these editors can suffer from suboptimal on-target performance. Here, we report the generation and characterization of CBEs that use engineered variants of TadA (CBE-T) that enable high on-target C·G to T·A across a sequence-diverse set of genomic loci, demonstrate robust activity in primary cells and cause no detectable elevation in genome-wide mutation. Additionally, we report cytosine and adenine base editors (CABEs) catalyzing both A-to-I and C-to-U editing (CABE-Ts). Together with ABEs, CBE-Ts and CABE-Ts enable the programmable installation of all transition mutations using laboratory-evolved TadA variants with improved properties relative to previously reported CBEs.


  • Organizational Affiliation

    Beam Therapeutics, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-specific adenosine deaminase 1.14
A, B
167Escherichia coliMutation(s): 0 
Gene Names: tadA
EC: 3.5.4.33
UniProt
Find proteins for P68398 (Escherichia coli (strain K12))
Explore P68398 
Go to UniProtKB:  P68398
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68398
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.74α = 90
b = 89.74β = 90
c = 112γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references, Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description