1L2I

Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide

• PDB DOI:  https://doi.org/10.2210/pdb1L2I/pdb

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


• Deposited: 2002-02-21 Released: 2002-05-01 
• Deposition Author(s): Shiau, A.K., Barstad, D., Radek, J.T., Meyers, M.J., Nettles, K.W., Katzenellenbogen, B.S., Katzenellenbogen, J.A., Agard, D.A., Greene, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.243 
• R-Value Work: 0.203 

Literature

Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism.

Shiau, A.K., Barstad, D., Radek, J.T., Meyers, M.J., Nettles, K.W., Katzenellenbogen, B.S., Katzenellenbogen, J.A., Agard, D.A., Greene, G.L.

(2002) Nat Struct Biol 9: 359-364

• PubMed: 11953755 
• DOI: https://doi.org/10.1038/nsb787
• Primary Citation of Related Structures:  
  1L2I, 1L2J


• PubMed Abstract: 
  

The R,R enantiomer of 5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol (THC) exerts opposite effects on the transcriptional activity of the two estrogen receptor (ER) subtypes, ER alpha and ER beta. THC acts as an ER alpha agonist and as an ER beta antagonist. We have determined the crystal structures of the ER alpha ligand binding domain (LBD) bound to both THC and a fragment of the transcriptional coactivator GRIP1, and the ER beta LBD bound to THC. THC stabilizes a conformation of the ER alpha LBD that permits coactivator association and a conformation of the ER beta LBD that prevents coactivator association. A comparison of the two structures, taken together with functional data, reveals that THC does not act on ER beta through the same mechanisms used by other known ER antagonists. Instead, THC antagonizes ER beta through a novel mechanism we term 'passive antagonism'.

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Related Citations: 

• The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of this Interaction by Tamoxifen
  Shiau, A.K., Barstad, D., Loria, P.M., Cheng, L., Kushner, P.J., Agard, D.A., Greene, G.L.
  (1998) Cell 95: 927

• Estrogen Receptor Subtype-selective Ligands: Asymmetric Synthesis and Biological Evaluation of cis- and trans-5,11-dialkyl-5,6,11,12-tetrahydrochrysenes
  Meyers, M.J., Sun, J., Carlson, K.E., Katzenellenbogen, B.S., Katzenellenbogen, J.A.
  (1999) J Med Chem 42: 2456

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Organizational Affiliation: 

The Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA.

Biological Assembly 1  

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.65 kDa 
• Atom Count: 4,043 
• Modelled Residue Count: 486 
• Deposited Residue Count: 548 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR	A, B	261	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOCORTICOID RECEPTOR-INTERACTING PROTEIN 1	C, D	13	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q61026 (Mus musculus) Explore Q61026  Go to UniProtKB:  Q61026
IMPC:  MGI:1276533

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETC	F [auth A], G [auth B]	(R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL C22 H24 O2 MASYAWHPJCQLSW-ZIAGYGMSSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS	A, B	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.243 
• R-Value Work: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.545	α = 90
b = 82.6	β = 111.53
c = 59.04	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-01 
Deposition Author(s): Shiau, A.K., Barstad, D., Radek, J.T., Meyers, M.J., Nettles, K.W., Katzenellenbogen, B.S., Katzenellenbogen, J.A., Agard, D.A., Greene, G.L.

Revision History  

• Version 1.0: 2002-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description