7NIX | pdb_00007nix

14-3-3 sigma with AS160 binding site pT642


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7NIX

This is version 1.3 of the entry. See complete history

Literature

Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions.

Cossar, P.J.Wolter, M.van Dijck, L.Valenti, D.Levy, L.M.Ottmann, C.Brunsveld, L.

(2021) J Am Chem Soc 143: 8454-8464

  • DOI: https://doi.org/10.1021/jacs.1c03035
  • Primary Citation Related Structures: 
    7AOG, 7AXN, 7AYF, 7AZ1, 7AZ2, 7BDP, 7BDT, 7BDY, 7BFW, 7BG3, 7BGQ, 7BGR, 7BGV, 7BGW, 7NIF, 7NIG, 7NIX, 7NJ6, 7NJ8, 7NJA, 7NQP, 7NRK, 7NRL, 7NSV

  • PubMed Abstract: 

    The stabilization of protein complexes has emerged as a promising modality, expanding the number of entry points for novel therapeutic intervention. Targeting proteins that mediate protein-protein interactions (PPIs), such as hub proteins, is equally challenging and rewarding as they offer an intervention platform for a variety of diseases, due to their large interactome. 14-3-3 hub proteins bind phosphorylated motifs of their interaction partners in a conserved binding channel. The 14-3-3 PPI interface is consequently only diversified by its different interaction partners. Therefore, it is essential to consider, additionally to the potency, also the selectivity of stabilizer molecules. Targeting a lysine residue at the interface of the composite 14-3-3 complex, which can be targeted explicitly via aldimine-forming fragments, we studied the de novo design of PPI stabilizers under consideration of potential selectivity. By applying cooperativity analysis of ternary complex formation, we developed a reversible covalent molecular glue for the 14-3-3/Pin1 interaction. This small fragment led to a more than 250-fold stabilization of the 14-3-3/Pin1 interaction by selective interfacing with a unique tryptophan in Pin1. This study illustrates how cooperative complex formation drives selective PPI stabilization. Further, it highlights how specific interactions within a hub proteins interactome can be stabilized over other interactions with a common binding motif.


  • Organizational Affiliation
    • Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 30.12 kDa 
  • Atom Count: 2,132 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 264 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein sigma253Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TBC1 domain family member 411Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60343 (Homo sapiens)
Explore O60343 
Go to UniProtKB:  O60343
PHAROS:  O60343
GTEx:  ENSG00000136111 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60343
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.219α = 90
b = 121.219β = 90
c = 74.464γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European Commission675179
H2020 Marie Curie Actions of the European Commission754462

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary