1M2Z

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

• PDB DOI:  https://doi.org/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.

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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: https://doi.org/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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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: 4,782 
• Modelled Residue Count: 550 
• Deposited Residue Count: 556 
• Unique protein chains: 2

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
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150

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

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

Binding Affinity Annotations
ID	Source	Binding Affinity
DEX	BindingDB:  1M2Z	Ki: min: 0.69, max: 6.8 (nM) from 9 assay(s)
		Kd: min: 2, max: 19 (nM) from 3 assay(s)
		IC50: min: 0.5, max: 22 (nM) from 29 assay(s)
		EC50: min: 0.1, max: 17 (nM) from 18 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 = 125.843	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

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