4HN6

GR DNA Binding Domain R460D/D462R - TSLP nGRE Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structural basis of direct glucocorticoid-mediated transrepression.

Hudson, W.H.Youn, C.Ortlund, E.A.

(2013) Nat Struct Mol Biol 20: 53-58

  • DOI: 10.1038/nsmb.2456
  • Primary Citation of Related Structures:  
    4HN5, 4HN6

  • PubMed Abstract: 
  • A newly discovered negative glucocorticoid response element (nGRE) mediates DNA-dependent transrepression by the glucocorticoid receptor (GR) across the genome and has a major role in immunosuppressive therapy. The nGRE differs dramatically from activating response elements, and the mechanism driving GR binding and transrepression is unknown ...

    A newly discovered negative glucocorticoid response element (nGRE) mediates DNA-dependent transrepression by the glucocorticoid receptor (GR) across the genome and has a major role in immunosuppressive therapy. The nGRE differs dramatically from activating response elements, and the mechanism driving GR binding and transrepression is unknown. To unravel the mechanism of nGRE-mediated transrepression by the GR, we characterized the interaction between GR and an nGRE in the thymic stromal lymphopoietin (TSLP) promoter. We show using structural and mechanistic approaches that nGRE binding is a new mode of sequence recognition by human GR and that nGREs prevent receptor dimerization through a unique GR-binding orientation and strong negative cooperativity, ensuring the presence of monomeric GR at repressive elements.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptorA,
D [auth B]
114Homo sapiensMutation(s): 2 
Gene Names: NR3C1GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
PHAROS:  P04150
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04150
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)-3')B [auth C]16synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*CP*TP*CP*TP*CP*CP*CP*GP*GP*AP*GP*GP*CP*G)-3')C [auth D]16synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.74α = 90
b = 87.87β = 90
c = 103.15γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Advisory, Structure summary