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: 60.71 kDa 
• Atom Count: 4140 
• Residue Count: 496 
• Unique protein chains: 2

4DMA

Crystal structure of ERa LBD in complex with RU100132

• DOI: 10.2210/pdb4DMA/pdb

• Classification: TRANSCRIPTION/protein binding/agonist
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-07 Released: 2012-03-07 
• Deposition Author(s): Osz, J., Brelivet, Y., Peluso-Iltis, C., Cura, V., Eiler, S., Ruff, M., Bourguet, W., Rochel, N., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Structural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors.

Osz, J., Brelivet, Y., Peluso-Iltis, C., Cura, V., Eiler, S., Ruff, M., Bourguet, W., Rochel, N., Moras, D.

(2012) Proc Natl Acad Sci U S A 109: E588-E594

• PubMed: 22355136 
• DOI: 10.1073/pnas.1118192109
• Primary Citation of Related Structures:  
  4DM6, 4DM8, 4DMA


• PubMed Abstract: 
  

Transcription regulation by steroid hormones, vitamin derivatives, and metabolites is mediated by nuclear receptors (NRs), which play an important role in ligand-dependent gene expression and human health. NRs function as homodimers or heterodimers and are involved in a combinatorial, coordinated and sequentially orchestrated exchange between coregulators (corepressors, coactivators). The architecture of DNA-bound functional dimers positions the coregulators proteins. We previously demonstrated that retinoic acid (RAR-RXR) and vitamin D3 receptors (VDR-RXR) heterodimers recruit only one coactivator molecule asymmetrically without steric hindrance for the binding of a second cofactor. We now address the problem of homodimers for which the presence of two identical targets enhances the functional importance of the mode of binding. Using structural and biophysical methods and RAR as a model, we could dissect the molecular mechanism of coactivator recruitment to homodimers. Our study reveals an allosteric mechanism whereby binding of a coactivator promotes formation of nonsymmetrical RAR homodimers with a 21 stoichiometry. Ligand conformation and the cofactor binding site of the unbound receptor are affected through the dimer interface. A similar control mechanism is observed with estrogen receptor (ER) thus validating the negative cooperativity model for an established functional homodimer. Correlation with published data on other NRs confirms the general character of this regulatory pathway.

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Related Citations: 

• Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERalpha in complex with synthetic ligands.
  Cura, V., Gangloff, M., Eiler, S., Moras, D., Ruff, M.
  (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 54

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Organizational Affiliation: 

Institut National de Santé et de Recherche Médicale U964/Centre National de Recherche Scientifique, Unité Mixte de Recherche 7104/Université de Strasbourg, 67404 Illkirch, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	247	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 1	E, F	15	Mus musculus	Mutation(s): 0  Gene Names: Ncoa1, Src1 EC: 2.3.1.48
Find proteins for P70365 (Mus musculus) Explore P70365  Go to UniProtKB:  P70365
NIH Common Fund Data Resources
IMPC  MGI:1276523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0L8	A, B	2'-bromo-6'-(furan-3-yl)-4'-(hydroxymethyl)biphenyl-4-ol C17 H13 Br O3 VXUYUWOEWFNCIK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.282	α = 90
b = 81.788	β = 111.17
c = 58.303	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-07 
• Released Date: 2012-03-07 
Deposition Author(s): Osz, J., Brelivet, Y., Peluso-Iltis, C., Cura, V., Eiler, S., Ruff, M., Bourguet, W., Rochel, N., Moras, D.

Revision History 

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Database references, Derived calculations