Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 59.63 kDa 
• Atom Count: 4149 
• Modelled Residue Count: 487 
• Deposited Residue Count: 514 
• Unique protein chains: 2

4IW6

Crystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with Constrained WAY-derivative, 7b

• DOI: 10.2210/pdb4IW6/pdb

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


• Deposited: 2013-01-23 Released: 2013-03-27 
• Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Parent, A.A., Cavett, V., Nowak, J., Hughes, T.S., Kojetin, D.J., Katzenellenbogen, J.A., Nettles, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

Ligand binding dynamics rewire cellular signaling via Estrogen Receptor-alpha

Srinivasan, S., Nwachukwu, J.C., Parent, A.A., Cavett, V., Nowak, J., Hughes, T.S., Kojetin, D.J., Katzenellenbogen, J.A., Nettles, K.W.

(2013) Nat Chem Biol 9: 326-332

• PubMed: 23524984 
• DOI: 10.1038/nchembio.1214
• Primary Citation of Related Structures:  
  4IWC, 4IWF, 4IVY, 4IW6, 4IVW, 4IW8, 4IU7, 4IV2, 4IV4, 4IUI


• PubMed Abstract: 
  

Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands). Proliferation of breast cancer cells directed by constrained ligands is associated with DNA binding, coactivator recruitment and activation of the estrogen-induced gene GREB1, reflecting a highly interconnected signaling network. In contrast, proliferation driven by dynamic ligands is associated with induction of ERα-mediated transcription in a DNA-binding domain (DBD)-dependent manner. Further, dynamic ligands showed enhanced anti-inflammatory activity. The DBD-dependent profile was predictive of these signaling patterns in a larger diverse set of natural and synthetic ligands. Thus, ligand dynamics directs unique signaling pathways and reveals a new role of the DBD in allosteric control of ERα-mediated signaling.

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Organizational Affiliation: 

Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, C [auth B]	247	Homo sapiens	Mutation(s): 1  Gene Names: ESR, ESR1, 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	B [auth C], D	10	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
1GU	E [auth A], F [auth B]	4-[2-(but-3-en-1-yl)-7-(trifluoromethyl)-2H-indazol-3-yl]benzene-1,3-diol C18 H15 F3 N2 O2 RKJSPKRUGGIGEE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.727	α = 90
b = 81.627	β = 109.77
c = 58.474	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-23 
• Released Date: 2013-03-27 
Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Parent, A.A., Cavett, V., Nowak, J., Hughes, T.S., Kojetin, D.J., Katzenellenbogen, J.A., Nettles, K.W.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Database references, Derived calculations