Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.18 kDa 
• Atom Count: 4782 
• Modelled Residue Count: 550 
• Deposited Residue Count: 556 
• Unique protein chains: 2

1M2Z

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

• DOI: 10.2210/pdb1M2Z/pdb

• Classification: HORMONE/HORMONE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-06-26 Released: 2003-07-15 
• Deposition Author(s): 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.

---

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 

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

• PubMed: 12151000 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucocorticoid receptor	A, C [auth D]	257	Homo sapiens	Mutation(s): 1  Gene Names: NR3C1, GRL
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS:  P04150 GTEx:  ENSG00000113580

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nuclear receptor coactivator 2	B, D [auth E]	21	N/A	Mutation(s): 0
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DEX	H [auth A], I [auth D]	DEXAMETHASONE C22 H29 F O5 UREBDLICKHMUKA-CXSFZGCWSA-N
BOG	E [auth A], F [auth A], G [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DEX	EC50:  1.100000023841858   nM  BindingDB
DEX	IC50:  1.2000000476837158   nM  BindingDB
DEX	IC50:  1.5800000429153442   nM  BindingDB
DEX	EC50:  7.199999809265137   nM  BindingDB
DEX	Ki:  6.699999809265137   nM  BindingDB
DEX	Ki:  1.2000000476837158   nM  BindingDB
DEX	EC50:  1   nM  BindingDB
DEX	IC50:  0.5   nM  BindingDB
DEX	Ki:  6.800000190734863   nM  BindingDB
DEX	IC50:  1.600000023841858   nM  BindingDB
DEX	IC50:  11.399999618530273   nM  BindingDB
DEX	EC50:  4.199999809265137   nM  BindingDB
DEX	IC50:  3.799999952316284   nM  BindingDB
DEX	EC50:  0.20000000298023224   nM  BindingDB
DEX	IC50:  1   nM  BindingDB
DEX	EC50:  1.7999999523162842   nM  BindingDB
DEX	Ki:  2.0999999046325684   nM  BindingDB
DEX	IC50:  4.099999904632568   nM  BindingDB
DEX	IC50:  7.599999904632568   nM  BindingDB
DEX	EC50:  5.010000228881836   nM  BindingDB
DEX	IC50:  2.509999990463257   nM  BindingDB
DEX	IC50:  6.099999904632568   nM  BindingDB
DEX	IC50:  22   nM  BindingDB
DEX	IC50:  2.5   nM  BindingDB
DEX	IC50:  3   nM  BindingDB
DEX	IC50:  0.5099999904632568   nM  BindingDB
DEX	EC50:  1.2999999523162842   nM  BindingDB
DEX	IC50:  3.5   nM  BindingDB
DEX	Ki:  5.5   nM  BindingDB
DEX	IC50:  1.399999976158142   nM  BindingDB
DEX	EC50:  7.940000057220459   nM  BindingDB
DEX	IC50:  5   nM  BindingDB
DEX	EC50:  13   nM  BindingDB
DEX	Ki:  0.6899999976158142   nM  BindingDB
DEX	IC50:  3.9800000190734863   nM  BindingDB
DEX	EC50:  17   nM  BindingDB
DEX	EC50:  6.900000095367432   nM  BindingDB
DEX	EC50:  9.699999809265137   nM  BindingDB
DEX	IC50:  1.1699999570846558   nM  BindingDB
DEX	Ki:  2.200000047683716   nM  BindingDB
DEX	EC50:  2.5   nM  BindingDB
DEX	EC50:  3.700000047683716   nM  BindingDB
DEX	Kd:  19   nM  BindingDB
DEX	IC50:  13   nM  BindingDB
DEX	IC50:  7.940000057220459   nM  BindingDB
DEX	Ki:  1.5   nM  BindingDB
DEX	IC50:  1.7999999523162842   nM  BindingDB
DEX	Ki:  1.100000023841858   nM  BindingDB
DEX	IC50:  21   nM  BindingDB
DEX	IC50:  2.4000000953674316   nM  BindingDB
DEX	IC50:  7.900000095367432   nM  BindingDB
DEX	EC50:  5   nM  BindingDB
DEX	IC50:  12.59000015258789   nM  BindingDB
DEX	EC50:  4.5   nM  BindingDB
DEX	IC50:  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 = 125.843	α = 90
b = 125.843	β = 90
c = 85.976	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-26 
• Released Date: 2003-07-15 
Deposition Author(s): 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.

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