4Q50 | pdb_00004q50

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 
    0.283 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4Q50

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 240.16 kDa 
  • Atom Count: 14,071 
  • Modeled Residue Count: 1,730 
  • Deposited Residue Count: 2,080 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OHT

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]
4-HYDROXYTAMOXIFEN
C26 H29 N O2
TXUZVZSFRXZGTL-QPLCGJKRSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth B],
R [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
OHT BindingDB:  4Q50 Ki: min: 0.04, max: 20 (nM) from 6 assay(s)
IC50: min: 0.31, max: 40 (nM) from 16 assay(s)
EC50: min: 6, max: 16 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
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
PHASERphasing
REFMACrefinement
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