8SVJ

Ubiquitin variant i53: mutant VHH with 53BP1 Tudor domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.210 

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
Tumor protein p53 binding protein 1124Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin varient i53 mutant VHH78Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for B4DV12 (Homo sapiens)
Explore B4DV12 
Go to UniProtKB:  B4DV12
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4DV12
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.98α = 90
b = 46.92β = 90
c = 90.57γ = 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, Refinement description