5V0L

Crystal structure of the AHR-ARNT heterodimer in complex with the DRE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex.

Seok, S.H.Lee, W.Jiang, L.Molugu, K.Zheng, A.Li, Y.Park, S.Bradfield, C.A.Xing, Y.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 5431-5436

  • DOI: 10.1073/pnas.1617035114

  • PubMed Abstract: 
  • The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metab ...

    The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metabolism, acute toxicity, to normal physiology of vascular and immune systems. The AHR forms a transcriptionally active heterodimer with ARNT (AHR nuclear translocator), which recognizes the dioxin response element (DRE) in the promoter of downstream genes. We determined the crystal structure of the mammalian AHR-ARNT heterodimer in complex with the DRE, in which ARNT curls around AHR into a highly intertwined asymmetric architecture, with extensive heterodimerization interfaces and AHR interdomain interactions. Specific recognition of the DRE is determined locally by the DNA-binding residues, which discriminates it from the closely related hypoxia response element (HRE), and is globally affected by the dimerization interfaces and interdomain interactions. Changes at the interdomain interactions caused either AHR constitutive nuclear localization or failure to translocate to nucleus, underlying an allosteric structural pathway for mediating ligand-induced exposure of nuclear localization signal. These observations, together with the global higher flexibility of the AHR PAS-A and its loosely packed structural elements, suggest a dynamic structural hierarchy for complex scenarios of AHR activation induced by its diverse ligands.


    Organizational Affiliation

    McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor nuclear translocator
A
279Homo sapiensMutation(s): 0 
Gene Names: ARNT (BHLHE2)
Find proteins for P27540 (Homo sapiens)
Go to Gene View: ARNT
Go to UniProtKB:  P27540
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor
B
241Mus musculusMutation(s): 0 
Gene Names: Ahr
Find proteins for P30561 (Mus musculus)
Go to UniProtKB:  P30561
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')C17Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')D14Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
B, C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.199α = 90.00
b = 64.364β = 100.14
c = 157.725γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM096060-01

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references
  • Version 1.2: 2017-06-07
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence