Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 32.94 kDa 
• Atom Count: 2136 
• Modelled Residue Count: 239 
• Deposited Residue Count: 280 
• Unique protein chains: 1

1NHZ

Crystal Structure of the Antagonist Form of Glucocorticoid Receptor

• PDB DOI: 10.2210/pdb1NHZ/pdb

• Classification: Hormone receptor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2002-12-20 Released: 2003-05-06 
• Deposition Author(s): Kauppi, B., Jakob, C., Farnegardh, M., Yang, J., Ahola, H., Alarcon, M., Calles, K., Engstrom, O., Harlan, J., Muchmore, S., Ramqvist, A.-K., Thorell, S., Ohman, L., Greer, J., Gustafsson, J.-A., Carlstedt-Duke, J., Carlquist, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

Literature

The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain: RU-486 INDUCES A TRANSCONFORMATION THAT LEADS TO ACTIVE ANTAGONISM.

Kauppi, B., Jakob, C., Farnegardh, M., Yang, J., Ahola, H., Alarcon, M., Calles, K., Engstrom, O., Harlan, J., Muchmore, S., Ramqvist, A.-K., Thorell, S., Ohman, L., Greer, J., Gustafsson, J.-A., Carlstedt-Duke, J., Carlquist, M.

(2003) J Biol Chem 278: 22748-22754

• PubMed: 12686538 
• DOI: 10.1074/jbc.M212711200
• Primary Citation of Related Structures:  
  1NHZ, 1P93


• PubMed Abstract: 
  

Here we describe the three-dimensional crystal structures of human glucocorticoid receptor ligand-binding domain (GR-LBD) in complex with the antagonist RU-486 at 2.3 A resolution and with the agonist dexamethasone ligand together with a coactivator peptide at 2.8 A. The RU-486 structure was solved in several different crystal forms, two with helix 12 intact (GR1 and GR3) and one with a protease-digested C terminus (GR2). In GR1, part of helix 12 is in a position that covers the co-activator pocket, whereas in the GR3, domain swapping is seen between the crystallographically identical subunits in the GR dimer. An arm consisting of the end of helix 11 and beyond stretches out from one molecule, and helix 12 binds to the other LBD, partly blocking the coactivator pocket of that molecule. This type of GR-LBD dimer has not been described before but might be an artifact from crystallization. Furthermore, the subunits of the GR3 dimers are covalently connected via a disulfide bond between the Cys-736 residues in the two molecules. All three RU-486 GR-LBD structures show that GR has a very flexible region between the end of helix 11 and the end of helix 12.

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Organizational Affiliation: 

Structure Biology, Karo Bio AB, Novum, SE-141 57 Huddinge, Sweden. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOCORTICOID RECEPTOR	A	280	Homo sapiens	Mutation(s): 3  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
486	B [auth A]	11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE C29 H35 N O2 VKHAHZOOUSRJNA-GCNJZUOMSA-N
HEZ	C [auth A], D [auth A], E [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
486	BindingDB:  1NHZ	Ki: min: 0.09, max: 169 (nM) from 18 assay(s)
		Kd: 15 (nM) from 1 assay(s)
		IC50: min: 8.00e-3, max: 33 (nM) from 31 assay(s)
		EC50: min: 0.6, max: 2500 (nM) from 6 assay(s)
	PDBBind:  1NHZ	Ki: 840 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.859	α = 90
b = 109.764	β = 90
c = 39.261	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-20 
• Released Date: 2003-05-06 
Deposition Author(s): Kauppi, B., Jakob, C., Farnegardh, M., Yang, J., Ahola, H., Alarcon, M., Calles, K., Engstrom, O., Harlan, J., Muchmore, S., Ramqvist, A.-K., Thorell, S., Ohman, L., Greer, J., Gustafsson, J.-A., Carlstedt-Duke, J., Carlquist, M.

Revision History  

• Version 1.0: 2003-05-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-09-02
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-27
  Changes: Database references