4ZPR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.272 

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:  
    4ZPH, 4ZP4, 4ZQD, 4ZPR, 4ZPK

  • 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

    Metabolic Disease Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocatorA384Mus musculusMutation(s): 0 
Gene Names: Arnt
Find proteins for P53762 (Mus musculus)
Explore P53762 
Go to UniProtKB:  P53762
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1-alphaB345Mus musculusMutation(s): 0 
Gene Names: Hif1a
Find proteins for Q61221 (Mus musculus)
Explore Q61221 
Go to UniProtKB:  Q61221
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
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
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.272 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.735α = 90
b = 66.735β = 90
c = 243.644γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CORELSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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