6CBZ

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Estradiol and GRIP Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Endoxifen, 4-Hydroxytamoxifen and an Estrogenic Derivative Modulate Estrogen Receptor Complex Mediated Apoptosis in Breast Cancer.

Maximov, P.Y.Abderrahman, B.Fanning, S.W.Sengupta, S.Fan, P.Curpan, R.F.Rincon, D.M.Q.Greenland, J.A.Rajan, S.S.Greene, G.L.Jordan, V.C.

(2018) Mol Pharmacol 94: 812-822

  • DOI: 10.1124/mol.117.111385
  • Primary Citation of Related Structures:  
    5T1Z, 5W9C, 5W9D, 6CBZ

  • PubMed Abstract: 
  • Estrogen therapy was used to treat advanced breast cancer in postmenopausal women for decades until the introduction of tamoxifen. Resistance to long-term estrogen deprivation (LTED) with tamoxifen and aromatase inhibitors used as a treatment of breast cancer inevitably occurs, but unexpectedly low-dose estrogen can cause regression of breast cancer and increase disease-free survival in some patients ...

    Estrogen therapy was used to treat advanced breast cancer in postmenopausal women for decades until the introduction of tamoxifen. Resistance to long-term estrogen deprivation (LTED) with tamoxifen and aromatase inhibitors used as a treatment of breast cancer inevitably occurs, but unexpectedly low-dose estrogen can cause regression of breast cancer and increase disease-free survival in some patients. This therapeutic effect is attributed to estrogen-induced apoptosis in LTED breast cancer. Here, we describe modulation of the estrogen receptor (ER) liganded with antiestrogens (endoxifen and 4-hydroxytamoxifen) and an estrogenic triphenylethylene (TPE), ethoxytriphenylethylene (EtOXTPE), on estrogen-induced apoptosis in LTED breast cancer cells. Our results show that the angular TPE estrogen (EtOXTPE) is able to induce the ER-mediated apoptosis only at a later time compared with planar estradiol in these cells. Using real-time polymerase chain reaction, chromatin immunoprecipitation, western blotting, molecular modeling, and X-ray crystallography techniques, we report novel conformations of the ER complex with an angular estrogen EtOXTPE and endoxifen. We propose that alteration of the conformation of the ER complexes, with changes in coactivator binding, governs estrogen-induced apoptosis through the protein kinase regulated by RNA-like endoplasmic reticulum kinase sensor system to trigger an unfolded protein response.


    Organizational Affiliation

    Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (P.Y.M., B.A., P.F., D.M.Q.R., J.A.G., V.C.J.); The Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois (S.W.F., S.S.R., G.L.G.); Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC (S.S.); and Institute of Chemistry, Romanian Academy, Timisoara, Romania (R.F.C.) VCJordan@mdanderson.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA250Homo 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorB250Homo 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
grip peptideC, D8Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  6CBZ 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: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.126α = 90
b = 84.621β = 108.48
c = 58.587γ = 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
Ludwig Center for Metastasis ResearchUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-21
    Changes: Data collection, Refinement description
  • Version 1.4: 2020-02-26
    Changes: Derived calculations