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 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/s41589-019-0234-5
  • Primary Citation of Related Structures:  
    6E3S, 6E3T, 6E3U

  • 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 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

    Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. dlwu@sdu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocator384Mus musculusMutation(s): 0 
Gene Names: Arnt
UniProt & NIH Common Fund Data Resources
Find proteins for P53762 (Mus musculus)
Explore P53762 
Go to UniProtKB:  P53762
IMPC:  MGI:88071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53762
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1368Mus musculusMutation(s): 1 
Gene Names: Epas1Hif2a
UniProt & NIH Common Fund Data Resources
Find proteins for P97481 (Mus musculus)
Explore P97481 
Go to UniProtKB:  P97481
IMPC:  MGI:109169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97481
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HNJ
Query on HNJ

Download Ideal Coordinates CCD File 
C [auth B]3-{[2-(pyrrolidin-1-yl)phenyl]amino}-1H-1lambda~6~,2-benzothiazole-1,1-dione
C17 H17 N3 O2 S
LONXCUOJVJLTIP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.951α = 90
b = 98.846β = 107.2
c = 77.077γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM117013, R01DK118297
National Science Foundation (NSF, China)China31700114

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description