245,392
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

1NHZ|pdb_00001nhz

Crystal Structure of the Antagonist Form of Glucocorticoid Receptor

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.276 (Depositor), 0.280 (DCC)
R-Value Work:
0.204 (Depositor), 0.220 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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 Biological Chem 278: 22748-22754

PubMed: 12686538 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

Structure Biology, Karo Bio AB, Novum, SE-141 57 Huddinge, Sweden. kauppi@karobio.se

Macromolecule Content

Total Structure Weight: 32.94 kDa
Atom Count: 2,136
Modeled Residue Count: 239
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOCORTICOID RECEPTOR	A	280	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150 Go to UniProtKB: P04150
PHAROS: P04150 GTEx: ENSG00000113580
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04150
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
486 Query on 486 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

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 33 assay(s)
		EC50: min: 0.6, max: 2500 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.276 (Depositor), 0.280 (DCC)
R-Value Work: 0.204 (Depositor), 0.220 (DCC)
R-Value Observed: 0.208 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-05-06

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.5: 2024-02-14
Changes: Data collection