5GTR | pdb_00005gtr

estrogen receptor alpha in complex with a stabilized peptide antagonist 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.367 (Depositor), 0.370 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5GTR

Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 29.18 kDa 
  • Atom Count: 1,974 
  • Modeled Residue Count: 246 
  • Deposited Residue Count: 253 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ARG-IAS-ILE-0JY-DPP-ARG-0JY-0JY-GLN-NH2B [auth C]10unidentifiedMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EST

Query on EST



Download:Ideal Coordinates CCD File
C [auth A]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DPP
Query on DPP
B [auth C]L-PEPTIDE LINKINGC3 H8 N2 O2ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.367 (Depositor), 0.370 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.787α = 90
b = 60.219β = 90
c = 66.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21102007 and 21372023

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Structure summary