6E3U

Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist M1001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bidirectional modulation of HIF-2 activity through chemical ligands.

Wu, D.Su, X.Lu, J.Li, S.Hood, B.L.Vasile, S.Potluri, N.Diao, X.Kim, Y.Khorasanizadeh, S.Rastinejad, F.

(2019) Nat. Chem. Biol. 15: 367-376

  • DOI: 10.1038/s41589-019-0234-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hypoxia-inducible factor-2 (HIF-2) is a heterodimeric transcription factor formed through dimerization between an oxygen-sensitive HIF-2α subunit and its obligate partner subunit ARNT. Enhanced HIF-2 activity drives some cancers, whereas reduced acti ...

    Hypoxia-inducible factor-2 (HIF-2) is a heterodimeric transcription factor formed through dimerization between an oxygen-sensitive HIF-2α subunit and its obligate partner subunit ARNT. Enhanced HIF-2 activity drives some cancers, whereas reduced activity causes anemia in chronic kidney disease. Therefore, modulation of HIF-2 activity via direct-binding ligands could provide many new therapeutic benefits. Here, we explored HIF-2α chemical ligands using combined crystallographic, biophysical, and cell-based functional studies. We found chemically unrelated antagonists to employ the same mechanism of action. Their binding displaced residue M252 from inside the HIF-2α PAS-B pocket toward the ARNT subunit to weaken heterodimerization. We also identified first-in-class HIF-2α agonists and found that they significantly displaced pocket residue Y281. Its dramatic side chain movement increases heterodimerization stability and transcriptional activity. Our findings show that despite binding to the same HIF-2α PAS-B pocket, ligands can manifest as inhibitors versus activators by mobilizing different pocket residues to allosterically alter HIF-2α-ARNT heterodimerization.


    Organizational Affiliation

    Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. dlwu@sdu.edu.cn.,Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA. fraydoon.rastinejad@ndm.ox.ac.uk.,Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA.,Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA.,Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA. dlwu@sdu.edu.cn.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK. fraydoon.rastinejad@ndm.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor nuclear translocator
A
384Mus musculusMutation(s): 0 
Gene Names: Arnt
Find proteins for P53762 (Mus musculus)
Go to UniProtKB:  P53762
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Endothelial PAS domain-containing protein 1
B
368Mus musculusMutation(s): 1 
Gene Names: Epas1 (Hif2a)
Find proteins for P97481 (Mus musculus)
Go to UniProtKB:  P97481
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HNJ
Query on HNJ

Download SDF File 
Download CCD File 
B
3-{[2-(pyrrolidin-1-yl)phenyl]amino}-1H-1lambda~6~,2-benzothiazole-1,1-dione
(3-Chloro-Phenyl)-acetic acid (S)-1-(2-tert-butoxycarbonylamino-acetyl)-pyrrolidin-2-ylmethyl ester
C17 H17 N3 O2 S
LONXCUOJVJLTIP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.951α = 90.00
b = 98.846β = 107.20
c = 77.077γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
Cootmodel building
PHASERphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01GM117013, R01DK118297
National Science Foundation (China)China31700114

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references
  • Version 1.2: 2019-04-03
    Type: Data collection, Database references