4HN6 | pdb_00004hn6

GR DNA Binding Domain R460D/D462R - TSLP nGRE Complex

• PDB DOI: https://doi.org/10.2210/pdb4HN6/pdb
• NAKB: 4HN6

• Classification: Transcription/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-18 Released: 2012-12-12 
• Deposition Author(s): Hudson, W.H., Youn, C.E., Ortlund, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

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

• PubMed: 23222642 
• DOI: https://doi.org/10.1038/nsmb.2456
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 35.58 kDa 
• Atom Count: 1,799 
• Modeled Residue Count: 176 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	A, D [auth B]	114	Homo sapiens	Mutation(s): 2  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)-3')	B [auth C]	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*TP*CP*TP*CP*CP*CP*GP*GP*AP*GP*GP*CP*G)-3')	C [auth D]	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.248 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.74	α = 90
b = 87.87	β = 90
c = 103.15	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Hudson, W.H., Youn, C.E., Ortlund, E.A.

Revision History  

• 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
• Version 1.4: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations