6PDZ

Crystal structure of PPARgamma ligand binding domain in complex with SMRT peptide and inverse agonist T0070907


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report



Literature

A molecular switch regulating transcriptional repression and activation of PPAR gamma.

Shang, J.Mosure, S.A.Zheng, J.Brust, R.Bass, J.Nichols, A.Solt, L.A.Griffin, P.R.Kojetin, D.J.

(2020) Nat Commun 11: 956-956

  • DOI: 10.1038/s41467-020-14750-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression ...

    Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression appears to occur through structurally diverse mechanisms. We report two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation. Helix 12 is displaced from the solvent-exposed active conformation and occupies the orthosteric ligand-binding pocket enabled by a conformational change that doubles the pocket volume. Paramagnetic relaxation enhancement (PRE) NMR and chemical crosslinking mass spectrometry confirm the repressive helix 12 conformation. PRE NMR also defines the mechanism of action of the corepressor-selective inverse agonist T0070907, and reveals that apo-helix 12 exchanges between transcriptionally active and repressive conformations-supporting a fundamental hypothesis in the NR field that helix 12 exchanges between transcriptionally active and repressive conformations.


    Organizational Affiliation

    Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA. dkojetin@scripps.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
275Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 2
C, D
22Homo sapiensMutation(s): 0 
Gene Names: NCOR2CTG26
Find proteins for Q9Y618 (Homo sapiens)
Go to UniProtKB:  Q9Y618
NIH Common Fund Data Resources
PHAROS  Q9Y618
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEY
Query on EEY

Download CCD File 
A, B
2-chloro-5-nitro-N-(pyridin-4-yl)benzamide
C12 H8 Cl N3 O3
FRPJSHKMZHWJBE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.756α = 90
b = 93.484β = 90
c = 114.607γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK101871

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release