8T2D

Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.

Perez-Bermejo, J.A.Efagene, O.Matern, W.M.Holden, J.K.Kabir, S.Chew, G.M.Andreoletti, G.Catton, E.Ennis, C.L.Garcia, A.Gerstenberg, T.L.Hill, K.A.Jain, A.Krassovsky, K.Lalisan, C.D.Lord, D.Quejarro, B.J.Sales-Lee, J.Shah, M.Silva, B.J.Skowronski, J.Strukov, Y.G.Thomas, J.Veraz, M.Vijay, T.Wallace, K.A.Yuan, Y.Grogan, J.L.Wienert, B.Lahiri, P.Treusch, S.Dever, D.P.Soros, V.B.Partridge, J.R.Seim, K.L.

(2024) Nat Commun 15: 2625-2625

  • DOI: https://doi.org/10.1038/s41467-024-46816-5
  • Primary Citation of Related Structures:  
    8SVG, 8SVH, 8SVI, 8SVJ, 8T2D

  • PubMed Abstract: 

    Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.


  • Organizational Affiliation

    Graphite Bio, South San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin variant i53A [auth B]78Homo sapiensMutation(s): 3 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor protein p53 binding protein 1B [auth A]124Homo sapiensMutation(s): 0 
Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens)
Explore Q12888 
Go to UniProtKB:  Q12888
PHAROS:  Q12888
GTEx:  ENSG00000067369 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12888
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.511α = 90
b = 46.855β = 90
c = 91.122γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references