Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.13 kDa 
• Atom Count: 2164 
• Modelled Residue Count: 221 
• Deposited Residue Count: 238 
• Unique protein chains: 2

3F1O

Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with an internally-bound artificial ligand

• PDB DOI: 10.2210/pdb3F1O/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-28 Released: 2009-01-20 
• Deposition Author(s): Scheuermann, T.H., Tomchick, D.R., Machius, M., Guo, Y., Bruick, R.K., Gardner, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.203 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.

Scheuermann, T.H., Tomchick, D.R., Machius, M., Guo, Y., Bruick, R.K., Gardner, K.H.

(2009) Proc Natl Acad Sci U S A 106: 450-455

• PubMed: 19129502 
• DOI: 10.1073/pnas.0808092106
• Primary Citation of Related Structures:  
  3F1N, 3F1O, 3F1P


• PubMed Abstract: 
  

The hypoxia-inducible factor (HIF) basic helix-loop-helix Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim (bHLH-PAS) transcription factors are master regulators of the conserved molecular mechanism by which metazoans sense and respond to reductions in local oxygen concentrations. In humans, HIF is critically important for the sustained growth and metastasis of solid tumors. Here, we describe crystal structures of the heterodimer formed by the C-terminal PAS domains from the HIF2alpha and ARNT subunits of the HIF2 transcription factor, both in the absence and presence of an artificial ligand. Unexpectedly, the HIF2alpha PAS-B domain contains a large internal cavity that accommodates ligands identified from a small-molecule screen. Binding one of these ligands to HIF2alpha PAS-B modulates the affinity of the HIF2alpha:ARNT PAS-B heterodimer in vitro. Given the essential role of PAS domains in forming active HIF heterodimers, these results suggest a presently uncharacterized ligand-mediated mechanism for regulating HIF2 activity in endogenous and clinical settings.

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Organizational Affiliation: 

Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	A	117	Homo sapiens	Mutation(s): 1  Gene Names: EPAS1, HIF2A, Hypoxia Inducible Factor 2 alpha, MOP2, BHLHE73, PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens) Explore Q99814  Go to UniProtKB:  Q99814
PHAROS:  Q99814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	B	121	Homo sapiens	Mutation(s): 1  Gene Names: ARNT, Aryl Hydrocarbon Receptor Nuclear Translocator, BHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens) Explore P27540  Go to UniProtKB:  P27540
PHAROS:  P27540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2XY	C [auth A]	N-[2-nitro-4-(trifluoromethyl)phenyl]morpholin-4-amine C11 H12 F3 N3 O3 XUPDNGHJBHPAKD-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.203 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.761	α = 90
b = 83.019	β = 106.36
c = 41.553	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-28 
• Released Date: 2009-01-20 
Deposition Author(s): Scheuermann, T.H., Tomchick, D.R., Machius, M., Guo, Y., Bruick, R.K., Gardner, K.H.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations