2GPP

Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation.

Wang, L.Zuercher, W.J.Consler, T.G.Lambert, M.H.Miller, A.B.Orband-Miller, L.A.McKee, D.D.Willson, T.M.Nolte, R.T.

(2006) J Biol Chem 281: 37773-37781

  • DOI: 10.1074/jbc.M608410200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • X-ray crystal structures of the ligand binding domain (LBD) of the estrogen-related receptor-gamma (ERRgamma) were determined that describe this receptor in three distinct states: unliganded, inverse agonist bound, and agonist bound. Two structures w ...

    X-ray crystal structures of the ligand binding domain (LBD) of the estrogen-related receptor-gamma (ERRgamma) were determined that describe this receptor in three distinct states: unliganded, inverse agonist bound, and agonist bound. Two structures were solved for the unliganded state, the ERRgamma LBD alone, and in complex with a coregulator peptide representing a portion of receptor interacting protein 140 (RIP140). No significant differences were seen between these structures that both exhibited the conformation of ERRgamma seen in studies with other coactivators. Two structures were obtained describing the inverse agonist-bound state, the ERRgamma LBD with 4-hydroxytamoxifen (4-OHT), and the ERRgamma LBD with 4-OHT and a peptide representing a portion of the silencing mediator of retinoid and thyroid hormone action protein (SMRT). The 4-OHT structure was similar to other reported inverse agonist bound structures, showing reorientation of phenylalanine 435 and a displacement of the AF-2 helix relative to the unliganded structures with little other rearrangement occurring. No significant changes to the LBD appear to be induced by peptide binding with the addition of the SMRT peptide to the ERRgamma plus 4-OHT complex. The observed agonist-bound state contains the ERRgamma LBD, a ligand (GSK4716), and the RIP140 peptide and reveals an unexpected rearrangement of the phenol-binding residues. Thermal stability studies show that agonist binding leads to global stabilization of the ligand binding domain. In contrast to the conventional mechanism of nuclear receptor ligand activation, activation of ERRgamma by GSK4716 does not appear to involve a major rearrangement or significant stabilization of the C-terminal helix.


    Organizational Affiliation

    Discovery Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27909, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen-related receptor gammaA, B230Homo sapiensMutation(s): 0 
Gene Names: ESRRGERR3ERRG2KIAA0832NR3B3
Find proteins for P62508 (Homo sapiens)
Explore P62508 
Go to UniProtKB:  P62508
NIH Common Fund Data Resources
PHAROS  P62508
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor-interacting protein 1C, D25N/AMutation(s): 0 
Find proteins for P48552 (Homo sapiens)
Explore P48552 
Go to UniProtKB:  P48552
NIH Common Fund Data Resources
PHAROS  P48552
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1BA
Query on 1BA

Download CCD File 
A
4-HYDROXY-N'-(4-ISOPROPYLBENZYL)BENZOHYDRAZIDE
C17 H20 N2 O2
MFDXHRPPSJRQFX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1BAIC50 :  2000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.81α = 90
b = 203.81β = 90
c = 53.46γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance