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URL: https://www.rcsb.org/structure/5E19

⇱ RCSB PDB - 5E19: Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative methyl {4-[bis(4-hydroxyphenyl)methylidene]cyclohexyl}acetate


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Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)

 5E19 | pdb_00005e19

Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative methyl {4-[bis(4-hydroxyphenyl)methylidene]cyclohexyl}acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Γ…
  • R-Value Free: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Predictive features of ligand-specific signaling through the estrogen receptor.

Nwachukwu, J.C.Srinivasan, S.Zheng, Y.Wang, S.Min, J.Dong, C.Liao, Z.Nowak, J.Wright, N.J.Houtman, R.Carlson, K.E.Josan, J.S.Elemento, O.Katzenellenbogen, J.A.Zhou, H.B.Nettles, K.W.

(2016) Mol Syst Biol 12: 864-864

  • PubMed27107013 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.15252/msb.20156701
  • Primary Citation Related Structures: 
    4ZN7, 4ZNH, 4ZNS, 4ZNT, 4ZNU, 4ZNV, 4ZNW, 5DI7, 5DID, 5DIE, 5DIG, 5DK9, 5DKB, 5DKE, 5DKG, 5DKS, 5DL4, 5DLR, 5DMC, 5DMF, 5DP0, 5DRJ, 5DRM, 5DTV, 5DU5, 5DUE, 5DUG, 5DUH, 5DVS, 5DVV, 5DWE, 5DWG, 5DWI, 5DWJ, 5DXK, 5DXM, 5DXP, 5DXQ, 5DXR, 5DY8, 5DYB, 5DYD, 5DZ0, 5DZ1, 5DZ3, 5DZH, 5DZI, 5E0W, 5E0X, 5E14, ... Search all related entries

  • PubMed Abstract: 

    Some estrogen receptor-Ξ± (ERΞ±)-targeted breast cancer therapies such as tamoxifen have tissue-selective or cell-specific activities, while others have similar activities in different cell types. To identify biophysical determinants of cell-specific signaling and breast cancer cell proliferation, we synthesized 241 ERΞ± ligands based on 19 chemical scaffolds, and compared ligand response using quantitative bioassays for canonical ERΞ± activities and X-ray crystallography. Ligands that regulate the dynamics and stability of the coactivator-binding site in the C-terminal ligand-binding domain, called activation function-2 (AF-2), showed similar activity profiles in different cell types. Such ligands induced breast cancer cell proliferation in a manner that was predicted by the canonical recruitment of the coactivators NCOA1/2/3 and induction of the GREB1 proliferative gene. For some ligand series, a single inter-atomic distance in the ligand-binding domain predicted their proliferative effects. In contrast, the N-terminal coactivator-binding site, activation function-1 (AF-1), determined cell-specific signaling induced by ligands that used alternate mechanisms to control cell proliferation. Thus, incorporating systems structural analyses with quantitative chemical biology reveals how ligands can achieve distinct allosteric signaling outcomes through ERΞ±.


  • Organizational Affiliation
    • Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA.
    • State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China.
    • Department of Chemistry, University of Illinois, Urbana, IL, USA.
    • PamGene International, Den Bosch, The Netherlands.
    • Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
    • Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA.
    • Department of Chemistry, University of Illinois, Urbana, IL, USA knettles@scripps.edu jkatzene@illinois.edu zhouhb@whu.edu.cn.
    • State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China knettles@scripps.edu jkatzene@illinois.edu zhouhb@whu.edu.cn.
    • Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA knettles@scripps.edu jkatzene@illinois.edu zhouhb@whu.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 62.64 kDa 
  • Atom Count: 3,974 
  • Modeled Residue Count: 490 
  • Deposited Residue Count: 542 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
257Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
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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
Nuclear receptor coactivator 2
C, D
14Homo sapiensMutation(s): 0 
πŸ‘ Image
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Γ…
  • R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Γ… )Angle ( ˚ )
a = 55.37Ξ± = 90
b = 81.998Ξ² = 110.83
c = 58.479Ξ³ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.