Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.11 kDa 
• Atom Count: 8331 
• Modelled Residue Count: 1022 
• Deposited Residue Count: 1168 
• Unique protein chains: 2

1P93

CRYSTAL STRUCTURE OF THE AGONIST FORM OF GLUCOCORTICOID RECEPTOR

• DOI: 10.2210/pdb1P93/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2003-05-09 Released: 2003-07-08 
• 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: 2.70 Å
• R-Value Free: 0.363 
• R-Value Work: 0.345 
• R-Value Observed: 0.350 

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, C [auth B], E [auth C], G [auth D]	280	Homo sapiens	Mutation(s): 3  Gene Names: NR3C1 or GRL, 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 [auth E], D [auth F], F [auth G], H	12	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DEX	I [auth A], J [auth B], K [auth C], L [auth D]	DEXAMETHASONE C22 H29 F O5 UREBDLICKHMUKA-CXSFZGCWSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DEX	EC50:  1   nM  BindingDB
DEX	Ki:  6.699999809265137   nM  BindingDB
DEX	IC50:  1.5800000429153442   nM  BindingDB
DEX	Ki:  1.100000023841858   nM  BindingDB
DEX	IC50:  1.2000000476837158   nM  BindingDB
DEX	IC50:  0.5   nM  BindingDB
DEX	Ki:  6.800000190734863   nM  BindingDB
DEX	IC50:  1.600000023841858   nM  BindingDB
DEX	EC50:  6.900000095367432   nM  BindingDB
DEX	EC50:  3.700000047683716   nM  BindingDB
DEX	Ki:  0.6899999976158142   nM  BindingDB
DEX	EC50:  7.199999809265137   nM  BindingDB
DEX	Ki:  2.200000047683716   nM  BindingDB
DEX	IC50:  1.7999999523162842   nM  BindingDB
DEX	Ki:  1.5   nM  BindingDB
DEX	EC50:  4.5   nM  BindingDB
DEX	EC50:  5   nM  BindingDB
DEX	IC50:  0.5099999904632568   nM  BindingDB
DEX	IC50:  13   nM  BindingDB
DEX	EC50:  9.699999809265137   nM  BindingDB
DEX	IC50:  1.1699999570846558   nM  BindingDB
DEX	IC50:  3.4000000953674316   nM  BindingDB
DEX	EC50:  2.5   nM  BindingDB
DEX	IC50:  7.900000095367432   nM  BindingDB
DEX	Kd:  19   nM  BindingDB
DEX	EC50:  1.100000023841858   nM  BindingDB
DEX	IC50:  21   nM  BindingDB
DEX	Kd :  19   nM  PDBBind
DEX	IC50:  2.4000000953674316   nM  BindingDB
DEX	Ki:  5.5   nM  BindingDB
DEX	IC50:  1.399999976158142   nM  BindingDB
DEX	EC50:  0.20000000298023224   nM  BindingDB
DEX	EC50:  1.2999999523162842   nM  BindingDB
DEX	EC50:  17   nM  BindingDB
DEX	IC50:  3.5   nM  BindingDB
DEX	IC50:  12.59000015258789   nM  BindingDB
DEX	IC50:  2.509999990463257   nM  BindingDB
DEX	IC50:  7.940000057220459   nM  BindingDB
DEX	IC50:  3   nM  BindingDB
DEX	IC50:  2.5   nM  BindingDB
DEX	IC50:  3.9800000190734863   nM  BindingDB
DEX	EC50:  7.940000057220459   nM  BindingDB
DEX	IC50:  5   nM  BindingDB
DEX	EC50:  13   nM  BindingDB
DEX	IC50:  1   nM  BindingDB
DEX	IC50:  6.099999904632568   nM  BindingDB
DEX	EC50:  4.199999809265137   nM  BindingDB
DEX	IC50:  7.599999904632568   nM  BindingDB
DEX	Ki:  1.2000000476837158   nM  BindingDB
DEX	IC50:  22   nM  BindingDB
DEX	Ki:  2.0999999046325684   nM  BindingDB
DEX	IC50:  3.799999952316284   nM  BindingDB
DEX	EC50:  5.010000228881836   nM  BindingDB
DEX	IC50:  11.399999618530273   nM  BindingDB
DEX	EC50:  1.7999999523162842   nM  BindingDB
DEX	IC50:  4.099999904632568   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.363 
• R-Value Work: 0.345 
• R-Value Observed: 0.350 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.4	α = 90
b = 127.4	β = 90
c = 91.8	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-09 
• Released Date: 2003-07-08 
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: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2020-09-02
  Changes: Data collection, Database references, Derived calculations, Structure summary