8EI4

Crystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.

Tokareva, O.S.Li, K.Travaline, T.L.Thomson, T.M.Swiecicki, J.M.Moussa, M.Ramirez, J.D.Litchman, S.Verdine, G.L.McGee, J.H.

(2023) Nat Commun 14: 6992-6992

  • DOI: https://doi.org/10.1038/s41467-023-42395-z
  • Primary Citation of Related Structures:  
    8EHZ, 8EI0, 8EI1, 8EI2, 8EI3, 8EI4, 8EI5, 8EI6, 8EI7, 8EI8, 8EI9, 8EIA, 8EIB, 8EIC

  • PubMed Abstract: 

    Molecules that induce novel interactions between proteins hold great promise for the study of biological systems and the development of therapeutics, but their discovery has been limited by the complexities of rationally designing interactions between three components, and because known binders to each protein are typically required to inform initial designs. Here, we report a general and rapid method for discovering α-helically constrained (Helicon) polypeptides that cooperatively induce the interaction between two target proteins without relying on previously known binders or an intrinsic affinity between the proteins. We show that Helicons are capable of binding every major class of E3 ubiquitin ligases, which are of great biological and therapeutic interest but remain largely intractable to targeting by small molecules. We then describe a phage-based screening method for discovering "trimerizer" Helicons, and apply it to reprogram E3s to cooperatively bind an enzyme (PPIA), a transcription factor (TEAD4), and a transcriptional coactivator (β-catenin).


  • Organizational Affiliation

    FOG Pharmaceuticals Inc., Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD4-like E3 ubiquitin-protein ligase WWP1376Homo sapiensMutation(s): 0 
Gene Names: WWP1
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0M0 (Homo sapiens)
Explore Q9H0M0 
Go to UniProtKB:  Q9H0M0
PHAROS:  Q9H0M0
GTEx:  ENSG00000123124 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0M0
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H30219synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.42α = 112.09
b = 51.21β = 99.61
c = 58.64γ = 102.51
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 privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references