Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66183.12 
• Atom Count: 4577 
• 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): 1 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.267 
• R-Value Work: 0.237 

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 


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
glucocorticoid receptor	A, D	257	Homo sapiens	Mutation(s): 1  Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens) Go to Gene View: NR3C1 Go to UniProtKB:  P04150

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
nuclear receptor coactivator 2	B, E	21	Homo sapiens	Mutation(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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DEX	A, D	DEXAMETHASONE 9A-FLUORO-16BETA-METHYLPREDNISOLONE C22 H29 F O5 UREBDLICKHMUKA-CXSFZGCWSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DEX	Kd: 19 nM (99) BINDINGDB
DEX	Ki: 0.7 - 6.8 nM (99) BINDINGDB
DEX	IC50: 0.5 - 21 nM (99) BINDINGDB
DEX	EC50: 0.2 - 17 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.267 
• R-Value Work: 0.237 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 125.843	α = 90.00
b = 125.843	β = 90.00
c = 85.976	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
HKL-2000	data collection
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Data collection