5Y7W

Crystal structure of the Nco-A1 PAS-B domain with YL-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeted Inhibition of the NCOA1/STAT6 Protein-Protein Interaction

Lee, Y.Yoon, H.Hwang, S.M.Shin, M.K.Lee, J.H.Oh, M.Im, S.H.Song, J.Lim, H.S.

(2017) J Am Chem Soc 139: 16056-16059

  • DOI: https://doi.org/10.1021/jacs.7b08972
  • Primary Citation of Related Structures:  
    5Y7W

  • PubMed Abstract: 

    The complex formation between transcription factors (TFs) and coactivator proteins is required for transcriptional activity, and thus disruption of aberrantly activated TF/coactivator interactions could be an attractive therapeutic strategy. However, modulation of such protein-protein interactions (PPIs) has proven challenging. Here we report a cell-permeable, proteolytically stable, stapled helical peptide directly targeting nuclear receptor coactivator 1 (NCOA1), a coactivator required for the transcriptional activity of signal transducer and activator of transcription 6 (STAT6). We demonstrate that this stapled peptide disrupts the NCOA1/STAT6 complex, thereby repressing STAT6-mediated transcription. Furthermore, we solved the first crystal structure of a stapled peptide in complex with NCOA1. The stapled peptide therefore represents an invaluable chemical probe for understanding the precise role of the NCOA1/STAT6 interaction and an excellent starting point for the development of a novel class of therapeutic agents.


  • Organizational Affiliation

    Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1
A, B
127Mus musculusMutation(s): 0 
Gene Names: Ncoa1Src1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for P70365 (Mus musculus)
Explore P70365 
Go to UniProtKB:  P70365
IMPC:  MGI:1276523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70365
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
YL-2 peptide
C, D
16synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALC
Query on ALC
C, D
L-PEPTIDE LINKINGC9 H17 N O2ALA
MK8
Query on MK8
C, D
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.501α = 90
b = 62.501β = 90
c = 137.177γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1A2B3004941
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9G4052952

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description