1P93

CRYSTAL STRUCTURE OF THE AGONIST FORM OF GLUCOCORTICOID RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.350 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    1NHZ, 1P93

  • 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 peptide at 2 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptorA, C [auth B], E [auth C], G [auth D]280Homo sapiensMutation(s): 3 
Gene Names: NR3C1 or GRLNR3C1GRL
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PHAROS:  P04150
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B [auth E], D [auth F], F [auth G], H12N/AMutation(s): 0 
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Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEX
Query on DEX

Download Ideal Coordinates CCD File 
I [auth A], J [auth B], K [auth C], L [auth D]DEXAMETHASONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DEXEC50:  1   nM  BindingDB
DEXKi:  6.699999809265137   nM  BindingDB
DEXIC50:  1.5800000429153442   nM  BindingDB
DEXKi:  1.100000023841858   nM  BindingDB
DEXIC50:  1.2000000476837158   nM  BindingDB
DEXIC50:  0.5   nM  BindingDB
DEXKi:  6.800000190734863   nM  BindingDB
DEXIC50:  1.600000023841858   nM  BindingDB
DEXEC50:  6.900000095367432   nM  BindingDB
DEXEC50:  3.700000047683716   nM  BindingDB
DEXKi:  0.6899999976158142   nM  BindingDB
DEXEC50:  7.199999809265137   nM  BindingDB
DEXKi:  2.200000047683716   nM  BindingDB
DEXIC50:  1.7999999523162842   nM  BindingDB
DEXKi:  1.5   nM  BindingDB
DEXEC50:  4.5   nM  BindingDB
DEXEC50:  5   nM  BindingDB
DEXIC50:  0.5099999904632568   nM  BindingDB
DEXIC50:  13   nM  BindingDB
DEXEC50:  9.699999809265137   nM  BindingDB
DEXIC50:  1.1699999570846558   nM  BindingDB
DEXIC50:  3.4000000953674316   nM  BindingDB
DEXEC50:  2.5   nM  BindingDB
DEXIC50:  7.900000095367432   nM  BindingDB
DEXKd:  19   nM  BindingDB
DEXEC50:  1.100000023841858   nM  BindingDB
DEXIC50:  21   nM  BindingDB
DEXKd :  19   nM  PDBBind
DEXIC50:  2.4000000953674316   nM  BindingDB
DEXKi:  5.5   nM  BindingDB
DEXIC50:  1.399999976158142   nM  BindingDB
DEXEC50:  0.20000000298023224   nM  BindingDB
DEXEC50:  1.2999999523162842   nM  BindingDB
DEXEC50:  17   nM  BindingDB
DEXIC50:  3.5   nM  BindingDB
DEXIC50:  12.59000015258789   nM  BindingDB
DEXIC50:  2.509999990463257   nM  BindingDB
DEXIC50:  7.940000057220459   nM  BindingDB
DEXIC50:  3   nM  BindingDB
DEXIC50:  2.5   nM  BindingDB
DEXIC50:  3.9800000190734863   nM  BindingDB
DEXEC50:  7.940000057220459   nM  BindingDB
DEXIC50:  5   nM  BindingDB
DEXEC50:  13   nM  BindingDB
DEXIC50:  1   nM  BindingDB
DEXIC50:  6.099999904632568   nM  BindingDB
DEXEC50:  4.199999809265137   nM  BindingDB
DEXIC50:  7.599999904632568   nM  BindingDB
DEXKi:  1.2000000476837158   nM  BindingDB
DEXIC50:  22   nM  BindingDB
DEXKi:  2.0999999046325684   nM  BindingDB
DEXIC50:  3.799999952316284   nM  BindingDB
DEXEC50:  5.010000228881836   nM  BindingDB
DEXIC50:  11.399999618530273   nM  BindingDB
DEXEC50:  1.7999999523162842   nM  BindingDB
DEXIC50:  4.099999904632568   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.350 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.4α = 90
b = 127.4β = 90
c = 91.8γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2020-09-02
    Changes: Data collection, Database references, Derived calculations, Structure summary