4ZPR

Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.902 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural integration in hypoxia-inducible factors.

Wu, D.Potluri, N.Lu, J.Kim, Y.Rastinejad, F.

(2015) Nature 524: 303-308

  • DOI: 10.1038/nature14883
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making ...

    The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making HIFs attractive anticancer targets. Transcriptionally active HIFs consist of HIF-α and ARNT (also called HIF-1β) subunits. Here we describe crystal structures for each of mouse HIF-2α-ARNT and HIF-1α-ARNT heterodimers in states that include bound small molecules and their hypoxia response element. A highly integrated quaternary architecture is shared by HIF-2α-ARNT and HIF-1α-ARNT, wherein ARNT spirals around the outside of each HIF-α subunit. Five distinct pockets are observed that permit small-molecule binding, including PAS domain encapsulated sites and an interfacial cavity formed through subunit heterodimerization. The DNA-reading head rotates, extends and cooperates with a distal PAS domain to bind hypoxia response elements. HIF-α mutations linked to human cancers map to sensitive sites that establish DNA binding and the stability of PAS domains and pockets.


    Organizational Affiliation

    Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.,Metabolic Disease Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827, USA.




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
Hypoxia-inducible factor 1-alpha
B
345Mus musculusMutation(s): 0 
Gene Names: Hif1a
Find proteins for Q61221 (Mus musculus)
Go to UniProtKB:  Q61221
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')C21Mus musculus
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')D21Mus musculus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.902 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.265 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 66.735α = 90.00
b = 66.735β = 90.00
c = 243.644γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
CORELSrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Refinement description