5GS4

Crystal structure of estrogen receptor alpha in complex with a stabilized peptide antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ESTClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Inhibition of ER alpha-Coactivator Interaction by High-Affinity N-Terminus Isoaspartic Acid Tethered Helical Peptides

Xie, M.Zhao, H.Liu, Q.Zhu, Y.Yin, F.Liang, Y.Jiang, Y.Wang, D.Hu, K.Qin, X.Wang, Z.Wu, Y.Xu, N.Ye, X.Wang, T.Li, Z.

(2017) J Med Chem 60: 8731-8740

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00732
  • Primary Citation of Related Structures:  
    5GS4, 5GTR

  • PubMed Abstract: 

    Direct inhibition of the protein-protein interaction of ERα and its endogenous coactivators with a cell permeable stabilized peptide may offer a novel, promising strategy for combating ERα positive breast cancers. Here, we report the co-crystal structure of a helical peptide stabilized by a N-terminal unnatural cross-linked aspartic acid (TD) in complex with the ERα ligand binding domain (LBD). We designed a series of peptides and peptide 6 that showed direct and high-affinity binding to ERα with selective antiproliferative activity in ERα positive breast cancer cells. The co-crystal structure of the TD-stabilized peptide 6 in complex with ERα LBD further demonstrates that it forms an α helical conformation and directly binds at the coactivator binding site of ERα. Further studies showed that peptide 6 W could potently inhibit cellular ERα's transcriptional activity. This approach demonstrates the potential of TD stabilized peptides to modulate various intracellular protein-protein interactions involved in a range of disorders.


  • Organizational Affiliation

    School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor243Homo sapiensMutation(s): 0 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-IAS-ILE-LEU-DNP-ARG-LEU-LEU-GLN10unidentifiedMutation(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: 2.40 Å
  • R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.272α = 90
b = 61.246β = 90
c = 69.385γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ESTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21102007 and 21372023
the Shenzhen Science and Technology Innovation CommitteeChina--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection