3MNP

Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, V708A, E711G) mutations at 1.50A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening.

Seitz, T.Thoma, R.Schoch, G.A.Stihle, M.Benz, J.D'Arcy, B.Wiget, A.Ruf, A.Hennig, M.Sterner, R.

(2010) J Mol Biol 403: 562-577

  • DOI: 10.1016/j.jmb.2010.08.048
  • Primary Citation of Related Structures:  
    3MNE, 3MNO, 3MNP

  • PubMed Abstract: 
  • The human glucocorticoid receptor ligand-binding domain (hGR-LBD) is an important drug target for the treatment of various diseases. However, the low intrinsic stability and solubility of hGR-LBD have rendered its purification and biophysical characterization difficult ...

    The human glucocorticoid receptor ligand-binding domain (hGR-LBD) is an important drug target for the treatment of various diseases. However, the low intrinsic stability and solubility of hGR-LBD have rendered its purification and biophysical characterization difficult. In order to overcome these problems, we have stabilized hGR-LBD by a combination of random mutagenesis and high-throughput screening using fluorescence-activated cell sorting (FACS) with enhanced green fluorescent protein (eGFP) as folding reporter. Two plasmid-encoded gene libraries of hGR-LBD fused to the egfp gene were expressed in Escherichia coli, followed by eight rounds of FACS screening, in each of which 10(8) cells were analyzed. The hgr-lbd mutants isolated by this approach contained numerous amino acid exchanges, and four beneficial ones (A605V, V702A, E705G, and M752T) were followed up in detail. Their characterization showed that the fluorescence of hGR-LBD-eGFP fusions is correlated linearly with the stability and solubility of hGR-LBD in the absence of eGFP. When combined, the four exchanges increased the thermal stability of hGR-LBD by more than 8 °C and enhanced its purification yield after expression in E. coli by about 26-fold. The introduction of three beneficial exchanges into the homologous ligand-binding domain of mouse enabled its X-ray structure determination at high resolution, which showed how the exchanges stabilize the protein and revealed atomic details that will guide future drug design. Our results demonstrate that large eGFP fusion libraries can be screened by FACS with extreme sensitivity and efficiency, yielding stabilized eukaryotic proteins suitable for biophysical characterization and structure determination.


    Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptorA261Mus musculusMutation(s): 3 
Gene Names: Nr3c1GrlGrl1
UniProt
Find proteins for P06537 (Mus musculus)
Explore P06537 
Go to UniProtKB:  P06537
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06537
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2 peptideB13Mus musculusMutation(s): 0 
Gene Names: Ncoa2Grip1Src2Tif2
UniProt & NIH Common Fund Data Resources
Find proteins for Q61026 (Mus musculus)
Explore Q61026 
Go to UniProtKB:  Q61026
IMPC:  MGI:1276533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61026
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEX
Query on DEX

Download Ideal Coordinates CCD File 
D [auth A]DEXAMETHASONE
C22 H29 F O5
UREBDLICKHMUKA-CXSFZGCWSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DEX BindingDB:  3MNP 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: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.089α = 90
b = 72.089β = 90
c = 128.827γ = 120
Software Package:
Software NamePurpose
PHASERphasing
BUSTER-TNTrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance