7V7L

Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of oleoylethanolamide as an endogenous ligand for HIF-3 alpha.

Diao, X.Ye, F.Zhang, M.Ren, X.Tian, X.Lu, J.Sun, X.Hou, Z.Chen, X.Li, F.Zhuang, J.Ding, H.Peng, C.Rastinejad, F.Luo, C.Wu, D.

(2022) Nat Commun 13: 2529-2529

  • DOI: https://doi.org/10.1038/s41467-022-30338-z
  • Primary Citation of Related Structures:  
    7V7L, 7V7W

  • PubMed Abstract: 

    Hypoxia-inducible factors (HIFs) are α/β heterodimeric transcription factors modulating cellular responses to the low oxygen condition. Among three HIF-α isoforms, HIF-3α is the least studied to date. Here we show that oleoylethanolamide (OEA), a physiological lipid known to regulate food intake and metabolism, binds selectively to HIF-3α. Through crystallographic analysis of HIF-3 α/β heterodimer in both apo and OEA-bound forms, hydrogen-deuterium exchange mass spectrometry (HDX-MS), molecular dynamics (MD) simulations, and biochemical and cell-based assays, we unveil the molecular mechanism of OEA entry and binding to the PAS-B pocket of HIF-3α, and show that it leads to enhanced heterodimer stability and functional modulation of HIF-3. The identification of HIF-3α as a selective lipid sensor is consistent with recent human genetic findings linking HIF-3α with obesity, and demonstrates that endogenous metabolites can directly interact with HIF-α proteins to modulate their activities, potentially as a regulatory mechanism supplementary to the well-known oxygen-dependent HIF-α hydroxylation.


  • Organizational Affiliation

    Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocator359Mus 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxia-inducible factor 3-alpha364Mus musculusMutation(s): 0 
Gene Names: Hif3a
UniProt
Find proteins for Q0VBL6 (Mus musculus)
Explore Q0VBL6 
Go to UniProtKB:  Q0VBL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0VBL6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.843α = 90
b = 86.291β = 90
c = 143.701γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22177063

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description