The Estrogen Receptor Alpha Ligand Binding Domain D538G Mutant in Complex with 4-hydroxytamoxifen

Experimental Data Snapshot

  • Resolution: 3.07 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation.

Fanning, S.W.Mayne, C.G.Dharmarajan, V.Carlson, K.E.Martin, T.A.Novick, S.J.Toy, W.Green, B.Panchamukhi, S.Katzenellenbogen, B.S.Tajkhorshid, E.Griffin, P.R.Shen, Y.Chandarlapaty, S.Katzenellenbogen, J.A.Greene, G.L.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.12792
  • Primary Citation of Related Structures:  
    4PXM, 4Q13, 4Q50

  • PubMed Abstract: 

    Somatic mutations in the estrogen receptor alpha (ERα) gene (ESR1), especially Y537S and D538G, have been linked to acquired resistance to endocrine therapies. Cell-based studies demonstrated that these mutants confer ERα constitutive activity and antiestrogen resistance and suggest that ligand-binding domain dysfunction leads to endocrine therapy resistance. Here, we integrate biophysical and structural biology data to reveal how these mutations lead to a constitutively active and antiestrogen-resistant ERα. We show that these mutant ERs recruit coactivator in the absence of hormone while their affinities for estrogen agonist (estradiol) and antagonist (4-hydroxytamoxifen) are reduced. Further, they confer antiestrogen resistance by altering the conformational dynamics of the loop connecting Helix 11 and Helix 12 in the ligand-binding domain of ERα, which leads to a stabilized agonist state and an altered antagonist state that resists inhibition.

  • Organizational Affiliation

    Ben May Department for Cancer Research, University of Chicago, Chicago, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B, C, D, E
A, B, C, D, E, F, G, H
260Homo sapiensMutation(s): 1 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OHT

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
L [auth C]
M [auth D]
N [auth E]
I [auth A],
J [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H]
C26 H29 N O2
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B],
R [auth H]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
OHT BindingDB:  4Q50 Ki: min: 0.04, max: 5.7 (nM) from 5 assay(s)
IC50: min: 0.31, max: 40 (nM) from 11 assay(s)
EC50: min: 6, max: 16 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.07 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.651α = 90
b = 165.244β = 90
c = 191.384γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations