1M2Z

Crystal structure of a dimer complex of the human glucocorticoid receptor ligand-binding domain bound to dexamethasone and a TIF2 coactivator motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Reveals a Novel Mode of Receptor Dimerization and Coactivator Recognition

Bledsoe, R.B.Montana, V.G.Stanley, T.B.Delves, C.J.Apolito, C.J.Mckee, D.D.Consler, T.G.Parks, D.J.Stewart, E.L.Willson, T.M.Lambert, M.H.Moore, J.T.Pearce, K.H.Xu, H.E.

(2002) Cell 110: 93-105

  • DOI: 10.1016/s0092-8674(02)00817-6
  • Primary Citation of Related Structures:  
    1M2Z

  • PubMed Abstract: 
  • Transcriptional regulation by the glucocorticoid receptor (GR) is mediated by hormone binding, receptor dimerization, and coactivator recruitment. Here, we report the crystal structure of the human GR ligand binding domain (LBD) bound to dexamethason ...

    Transcriptional regulation by the glucocorticoid receptor (GR) is mediated by hormone binding, receptor dimerization, and coactivator recruitment. Here, we report the crystal structure of the human GR ligand binding domain (LBD) bound to dexamethasone and a coactivator motif derived from the transcriptional intermediary factor 2. Despite structural similarity to other steroid receptors, the GR LBD adopts a surprising dimer configuration involving formation of an intermolecular beta sheet. Functional studies demonstrate that the novel dimer interface is important for GR-mediated activation. The structure also reveals an additional charge clamp that determines the binding selectivity of a coactivator and a distinct ligand binding pocket that explains its selectivity for endogenous steroid hormones. These results establish a framework for understanding the roles of protein-hormone and protein-protein interactions in GR signaling pathways.


    Organizational Affiliation

    Gene Expression and Protein Biochemistry, Research Triangle Park, NC 27709, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glucocorticoid receptorAD257Homo sapiensMutation(s): 1 
Gene Names: NR3C1GRL
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS  P04150
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nuclear receptor coactivator 2BE21N/AMutation(s): 0 
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEX
Query on DEX

Download CCD File 
A, D
DEXAMETHASONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DEXEC50:  1.100000023841858   nM  BindingDB
DEXIC50:  1.2000000476837158   nM  BindingDB
DEXIC50:  1.5800000429153442   nM  BindingDB
DEXEC50:  7.199999809265137   nM  BindingDB
DEXKi:  6.699999809265137   nM  BindingDB
DEXKi:  1.2000000476837158   nM  BindingDB
DEXEC50:  1   nM  BindingDB
DEXIC50:  0.5   nM  BindingDB
DEXKi:  6.800000190734863   nM  BindingDB
DEXIC50:  1.600000023841858   nM  BindingDB
DEXIC50:  11.399999618530273   nM  BindingDB
DEXEC50:  4.199999809265137   nM  BindingDB
DEXIC50:  3.799999952316284   nM  BindingDB
DEXEC50:  0.20000000298023224   nM  BindingDB
DEXIC50:  1   nM  BindingDB
DEXEC50:  1.7999999523162842   nM  BindingDB
DEXKi:  2.0999999046325684   nM  BindingDB
DEXIC50:  4.099999904632568   nM  BindingDB
DEXIC50:  7.599999904632568   nM  BindingDB
DEXEC50:  5.010000228881836   nM  BindingDB
DEXIC50:  2.509999990463257   nM  BindingDB
DEXIC50:  6.099999904632568   nM  BindingDB
DEXIC50:  22   nM  BindingDB
DEXIC50:  2.5   nM  BindingDB
DEXIC50:  3   nM  BindingDB
DEXIC50:  0.5099999904632568   nM  BindingDB
DEXEC50:  1.2999999523162842   nM  BindingDB
DEXIC50:  3.5   nM  BindingDB
DEXKi:  5.5   nM  BindingDB
DEXIC50:  1.399999976158142   nM  BindingDB
DEXEC50:  7.940000057220459   nM  BindingDB
DEXIC50:  5   nM  BindingDB
DEXEC50:  13   nM  BindingDB
DEXKi:  0.6899999976158142   nM  BindingDB
DEXIC50:  3.9800000190734863   nM  BindingDB
DEXEC50:  17   nM  BindingDB
DEXEC50:  6.900000095367432   nM  BindingDB
DEXEC50:  9.699999809265137   nM  BindingDB
DEXIC50:  1.1699999570846558   nM  BindingDB
DEXKi:  2.200000047683716   nM  BindingDB
DEXEC50:  2.5   nM  BindingDB
DEXEC50:  3.700000047683716   nM  BindingDB
DEXKd:  19   nM  BindingDB
DEXIC50:  13   nM  BindingDB
DEXIC50:  7.940000057220459   nM  BindingDB
DEXKi:  1.5   nM  BindingDB
DEXIC50:  1.7999999523162842   nM  BindingDB
DEXKi:  1.100000023841858   nM  BindingDB
DEXIC50:  21   nM  BindingDB
DEXIC50:  2.4000000953674316   nM  BindingDB
DEXIC50:  7.900000095367432   nM  BindingDB
DEXEC50:  5   nM  BindingDB
DEXIC50:  12.59000015258789   nM  BindingDB
DEXEC50:  4.5   nM  BindingDB
DEXIC50:  3.4000000953674316   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.267 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.843α = 90
b = 125.843β = 90
c = 85.976γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-15
    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: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary