Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | 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

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
486	Ki:  0.09000000357627869   nM  BindingDB
486	Ki:  0.8199999928474426   nM  BindingDB
486	IC50:  3.200000047683716   nM  BindingDB
486	IC50:  1   nM  BindingDB
486	IC50:  20   nM  BindingDB
486	Ki:  0.23999999463558197   nM  BindingDB
486	EC50:  872   nM  BindingDB
486	EC50:  2   nM  BindingDB
486	EC50:  2.5   nM  BindingDB
486	IC50:  6.900000095367432   nM  BindingDB
486	Ki:  169   nM  BindingDB
486	Ki :  840   nM  PDBBind
486	IC50:  33   nM  BindingDB
486	Ki:  1   nM  BindingDB
486	IC50:  5   nM  BindingDB
486	IC50:  0.800000011920929   nM  BindingDB
486	IC50:  1.899999976158142   nM  BindingDB
486	IC50:  5.75   nM  BindingDB
486	Ki:  120   nM  BindingDB
486	IC50:  6   nM  BindingDB
486	IC50:  1.600000023841858   nM  BindingDB
486	EC50:  2500   nM  BindingDB
486	IC50:  8.699999809265137   nM  BindingDB
486	Ki:  0.10000000149011612   nM  BindingDB
486	Ki:  0.4399999976158142   nM  BindingDB
486	IC50:  0.30000001192092896   nM  BindingDB
486	IC50:  1.100000023841858   nM  BindingDB
486	IC50:  6.309999942779541   nM  BindingDB
486	IC50:  1.399999976158142   nM  BindingDB
486	IC50:  18   nM  BindingDB
486	IC50:  15   nM  BindingDB
486	Ki:  1.2000000476837158   nM  BindingDB
486	IC50:  0.6000000238418579   nM  BindingDB
486	IC50:  0.009999999776482582   nM  BindingDB
486	EC50:  4.800000190734863   nM  BindingDB
486	IC50:  4.679999828338623   nM  BindingDB
486	IC50:  4.699999809265137   nM  BindingDB
486	IC50:  3.299999952316284   nM  BindingDB
486	IC50:  13   nM  BindingDB
486	Ki:  0.4000000059604645   nM  BindingDB
486	Ki:  0.8399999737739563   nM  BindingDB
486	IC50:  11   nM  BindingDB
486	EC50:  0.6000000238418579   nM  BindingDB
486	Ki:  1.100000023841858   nM  BindingDB
486	Ki:  0.6800000071525574   nM  BindingDB
486	Ki:  6   nM  BindingDB
486	Ki:  0.30000001192092896   nM  BindingDB
486	IC50:  2.200000047683716   nM  BindingDB
486	IC50:  0.949999988079071   nM  BindingDB
486	Ki:  0.10000000149011612   nM  BindingDB
486	IC50:  5.800000190734863   nM  BindingDB
486	Ki:  3   nM  BindingDB
486	Ki:  5   nM  BindingDB
486	IC50:  4.800000190734863   nM  BindingDB

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