Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.57 kDa 
• Atom Count: 3930 
• Residue Count: 489 
• Unique protein chains: 2

5DXM

Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol

• DOI: 10.2210/pdb5DXM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-09-23 Released: 2016-05-04 
• Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Zheng, Y., Wang, S., Min, J., Dong, C., Liao, Z., Cavett, V., Nowak, J., Houtman, R., Carlson, K.E., Josan, J.S., Elemento, O., Katzenellenbogen, J.A., Zhou, H.B., Nettles, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

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

• PubMed: 27107013 
• DOI: 10.15252/msb.20156701
• Primary Citation of Related Structures:  
  5DIE, 5DID, 5DIG, 5EGV, 5EI1, 5EHJ, 5EIT, 4ZN7, 4ZNS, 4ZNT


• PubMed Abstract: 
  

Some estrogen receptor-α (ERα)-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 ERα ligands based on 19 chemical scaffolds, and compared ligand response using quantitative bioassays for canonical ERα 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 ERα.

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Organizational Affiliation: 

Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	257	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372 GTEx  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D	14	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596 GTEx  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5J0	A, B	3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol C22 H24 O2 MPHSLLGYXNIWMO-MVFCNCFGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.506	α = 90
b = 82.034	β = 111.06
c = 58.843	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-23 
• Released Date: 2016-05-04 
Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Zheng, Y., Wang, S., Min, J., Dong, C., Liao, Z., Cavett, V., Nowak, J., Houtman, R., Carlson, K.E., Josan, J.S., Elemento, O., Katzenellenbogen, J.A., Zhou, H.B., Nettles, K.W.

Revision History 

• Version 1.0: 2016-05-04
  Type: Initial release