4PXM

The Estrogen Receptor Alpha Ligand Binding Domain D538G Mutant in Complex with Estradiol and a glucocorticoid receptor-interacting protein 1 NR box II peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA, B271Homo sapiensMutation(s): 1 
Gene Names: ESR, ESR1, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2C, D13Homo sapiensMutation(s): 0 
Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  4PXM Ki: min: 0.11, max: 100 (nM) from 13 assay(s)
Kd: min: 0.2, max: 100 (nM) from 4 assay(s)
IC50: min: 1.00e-2, max: 46 (nM) from 46 assay(s)
EC50: min: 4.00e-3, max: 10 (nM) from 52 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.084α = 90
b = 84.182β = 108.83
c = 58.372γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Structure summary