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 

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This is version 1.5 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 dexamethasone and a coactivator motif derived from the transcriptional intermediary factor 2 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glucocorticoid receptorA, C [auth D]257Homo sapiensMutation(s): 1 
Gene Names: NR3C1GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
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 2B, D [auth E]21N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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
Binding Affinity Annotations 
IDSourceBinding Affinity
DEX BindingDB:  1M2Z Ki: min: 0.69, max: 6.8 (nM) from 9 assay(s)
Kd: 19 (nM) from 1 assay(s)
IC50: min: 0.5, max: 22 (nM) from 29 assay(s)
EC50: min: 0.2, max: 17 (nM) from 17 assay(s)
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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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2021-10-27
    Changes: Database references, Structure summary