1P93

CRYSTAL STRUCTURE OF THE AGONIST FORM OF GLUCOCORTICOID RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.345 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain: RU-486 INDUCES A TRANSCONFORMATION THAT LEADS TO ACTIVE ANTAGONISM.

Kauppi, B.Jakob, C.Farnegardh, M.Yang, J.Ahola, H.Alarcon, M.Calles, K.Engstrom, O.Harlan, J.Muchmore, S.Ramqvist, A.-K.Thorell, S.Ohman, L.Greer, J.Gustafsson, J.-A.Carlstedt-Duke, J.Carlquist, M.

(2003) J.Biol.Chem. 278: 22748-22754

  • DOI: 10.1074/jbc.M212711200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here we describe the three-dimensional crystal structures of human glucocorticoid receptor ligand-binding domain (GR-LBD) in complex with the antagonist RU-486 at 2.3 A resolution and with the agonist dexamethasone ligand together with a coactivator ...

    Here we describe the three-dimensional crystal structures of human glucocorticoid receptor ligand-binding domain (GR-LBD) in complex with the antagonist RU-486 at 2.3 A resolution and with the agonist dexamethasone ligand together with a coactivator peptide at 2.8 A. The RU-486 structure was solved in several different crystal forms, two with helix 12 intact (GR1 and GR3) and one with a protease-digested C terminus (GR2). In GR1, part of helix 12 is in a position that covers the co-activator pocket, whereas in the GR3, domain swapping is seen between the crystallographically identical subunits in the GR dimer. An arm consisting of the end of helix 11 and beyond stretches out from one molecule, and helix 12 binds to the other LBD, partly blocking the coactivator pocket of that molecule. This type of GR-LBD dimer has not been described before but might be an artifact from crystallization. Furthermore, the subunits of the GR3 dimers are covalently connected via a disulfide bond between the Cys-736 residues in the two molecules. All three RU-486 GR-LBD structures show that GR has a very flexible region between the end of helix 11 and the end of helix 12.


    Organizational Affiliation

    Structure Biology, Karo Bio AB, Novum, SE-141 57 Huddinge, Sweden. kauppi@karobio.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B, C, D
280Homo sapiensMutation(s): 3 
Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
E, F, G, H
12Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEX
Query on DEX

Download SDF File 
Download CCD File 
A, B, C, D
DEXAMETHASONE
9A-FLUORO-16BETA-METHYLPREDNISOLONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.345 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 127.400α = 90.00
b = 127.400β = 90.00
c = 91.800γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
CCP4data scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation