PDBsum entry 2a24

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protein Protein-protein interface(s) links
Transcription PDB id
Protein chains
107 a.a. *
108 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Haddock structure of hif-2a/arnt pas-b heterodimer
Structure: Endothelial pas domain protein 1. Chain: a. Fragment: c-terminal pas domain (pas-b). Synonym: epas-1, member of pas protein 2, mop2, hypoxia- inducible factor 2 alpha, hif-2 alpha, hif2 alpha, hif-1 alpha-like factor, hlf. Aryl hydrocarbon receptor nuclear translocator. Chain: b. Fragment: c-terminal pas domain (pas-b).
Source: Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606
NMR struc: 20 models
Authors: P.B.Card,P.J.Erbel,K.H.Gardner
Key ref:
P.B.Card et al. (2005). Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization. J Mol Biol, 353, 664-677. PubMed id: 16181639 DOI: 10.1016/j.jmb.2005.08.043
21-Jun-05     Release date:   17-Jan-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q99814  (EPAS1_HUMAN) -  Endothelial PAS domain-containing protein 1
870 a.a.
107 a.a.
Protein chain
Pfam   ArchSchema ?
P27540  (ARNT_HUMAN) -  Aryl hydrocarbon receptor nuclear translocator
789 a.a.
108 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 
  Biochemical function     signal transducer activity     1 term  


DOI no: 10.1016/j.jmb.2005.08.043 J Mol Biol 353:664-677 (2005)
PubMed id: 16181639  
Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization.
P.B.Card, P.J.Erbel, K.H.Gardner.
The aryl hydrocarbon receptor nuclear translocator (ARNT) is a promiscuous bHLH-PAS (Per-ARNT-Sim) protein that forms heterodimeric transcriptional regulator complexes with several other bHLH-PAS subunits to control a variety of biological pathways, some of which are centrally involved in disease initiation and/or progression. One of these is the hypoxia response pathway, which allows eukaryotic cells to respond to low oxygen tension via the formation of a heterodimeric complex between ARNT and another bHLH-PAS protein, the hypoxia-inducible factor alpha (HIF-alpha). We have previously shown that the C-terminal PAS domains of an HIF-alpha isoform (HIF-2alpha) and ARNT interact in vitro, and that mutations in the solvent-exposed beta-sheet surface of the HIF-2alpha domain not only disrupt this interaction, but also greatly attenuate the hypoxia response in living cells. Here, we have solved the solution structure of the corresponding PAS domain of ARNT and show that it utilizes a very similar interface for the interaction with the HIF-2alpha PAS domain. We also show that this domain self-associates in a concentration-dependent manner, and that the interface used in this homodimeric complex is very similar to that used in the formation of heterodimer. In addition, using experimentally derived NMR restraints, we used the program HADDOCK to calculate a low-resolution model of the complex formed in solution by these two PAS domains, and confirm the validity of this model using site-directed spin labeling to obtain long-range distance information in solution. With this information, we propose a model for the mode of multi-PAS domain interaction in bHLH-PAS transcriptional activation complexes.
  Selected figure(s)  
Figure 1.
Figure 1. Regulation of the hypoxia-inducible factor (HIF) by intracellular oxygen levels. Under normoxia, O[2]-dependent modifications target HIF-α subunits (green) for proteosomal degradation and interfere with their ability to interact with CBP/p300 transcriptional coactivators. Under the low O[2] levels of hypoxic conditions, HIF-α monomers are stabilized and transported to the nucleus where they form functional heterodimers with ARNT (blue) on hypoxia-responsive elements (HREs), upregulating gene transcription via the activity of their transcriptional activation domains (TADs, including ARNT TAD and HIF-α N and C-terminal TADs (NTAD and CTAD, respectively)).
Figure 4.
Figure 4. HADDOCK-derived structure of the HIF-2a/ARNT PAS-B domain complex. (a) Superposition of 20 lowest energy structures of the HIF-2a/ARNT PAS-B complex, with HIF-2a shown in green and ARNT in blue. The structure closest to the mean is highlighted with a tube representation for the backbone, and yellow sticks indicate the locations of the side-chains of three HIF-2a PAS-B residues previously shown to be critical for heterodimer formation and HIF-driven transcriptional activation.15^ and 16 (b) Ribbon diagram of the lowest energy complex structure (backbone r.m.s.d.=1.05(±0.31) Å for ordered residues 242-342 for HIF-2a and 361-445, 456-463 for ARNT PAS-B, relative to other members of ensemble). Backbone amide sites that display significant changes in chemical shift or intensity upon complex formation (shown as spheres) define the primary interface used for the HADDOCK calculations.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 664-677) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21512126 C.L.Partch, and K.H.Gardner (2011).
Coactivators necessary for transcriptional output of the hypoxia inducible factor, HIF, are directly recruited by ARNT PAS-B.
  Proc Natl Acad Sci U S A, 108, 7739-7744.  
21245039 N.Hao, M.L.Whitelaw, K.E.Shearwin, I.B.Dodd, and A.Chapman-Smith (2011).
Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR.
  Nucleic Acids Res, 39, 3695-3709.  
20148691 B.E.McIntosh, J.B.Hogenesch, and C.A.Bradfield (2010).
Mammalian Per-Arnt-Sim proteins in environmental adaptation.
  Annu Rev Physiol, 72, 625-645.  
  20112293 C.L.Partch, and K.H.Gardner (2010).
Coactivator recruitment: a new role for PAS domains in transcriptional regulation by the bHLH-PAS family.
  J Cell Physiol, 223, 553-557.  
  20205712 C.Wotzlaw, S.Gneuss, R.Konietzny, and J.Fandrey (2010).
Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software.
  PMC Biophys, 3, 5.  
19906177 P.Slavny, R.Little, P.Salinas, T.A.Clarke, and R.Dixon (2010).
Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein.
  Mol Microbiol, 75, 61-75.  
19894043 S.M.Nabuurs, Kort, A.H.Westphal, and C.P.van Mierlo (2010).
Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement.
  Eur Biophys J, 39, 689-698.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
19456125 A.Pandini, A.A.Soshilov, Y.Song, J.Zhao, L.Bonati, and M.S.Denison (2009).
Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis.
  Biochemistry, 48, 5972-5983.  
19324882 C.L.Partch, P.B.Card, C.A.Amezcua, and K.H.Gardner (2009).
Molecular Basis of Coiled Coil Coactivator Recruitment by the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT).
  J Biol Chem, 284, 15184-15192.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
19712683 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, L.Li, B.R.Crane, and L.Pollack (2009).
Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
  J Mol Biol, 393, 909-919.
PDB code: 3is2
19805192 K.Lee, H.Zhang, D.Z.Qian, S.Rey, J.O.Liu, and G.L.Semenza (2009).
Acriflavine inhibits HIF-1 dimerization, tumor growth, and vascularization.
  Proc Natl Acad Sci U S A, 106, 17910-17915.  
19196990 M.R.Evans, P.B.Card, and K.H.Gardner (2009).
ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space.
  Proc Natl Acad Sci U S A, 106, 2617-2622.
PDB code: 2k7s
19402751 S.Hennig, H.M.Strauss, K.Vanselow, O.Yildiz, S.Schulze, J.Arens, A.Kramer, and E.Wolf (2009).
Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2.
  PLoS Biol, 7, e94.
PDB codes: 3gdi 3gec
19129502 T.H.Scheuermann, D.R.Tomchick, M.Machius, Y.Guo, R.K.Bruick, and K.H.Gardner (2009).
Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.
  Proc Natl Acad Sci U S A, 106, 450-455.
PDB codes: 3f1n 3f1o 3f1p
18553928 B.D.Zoltowski, and B.R.Crane (2008).
Light activation of the LOV protein vivid generates a rapidly exchanging dimer.
  Biochemistry, 47, 7012-7019.
PDB code: 3d72
18096572 E.J.Dougherty, and R.S.Pollenz (2008).
Analysis of Ah receptor-ARNT and Ah receptor-ARNT2 complexes in vitro and in cell culture.
  Toxicol Sci, 103, 191-206.  
18931781 G.M.Clore (2008).
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement.
  Mol Biosyst, 4, 1058-1069.  
18560762 H.E.Lindfors, Koning, J.W.Drijfhout, B.Venezia, and M.Ubbink (2008).
Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR.
  J Biomol NMR, 41, 157-167.  
18715002 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, B.R.Crane, and L.Pollack (2008).
Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle X-ray scattering.
  J Am Chem Soc, 130, 12226-12227.  
18942854 R.A.Ayers, and K.Moffat (2008).
Changes in quaternary structure in the signaling mechanisms of PAS domains.
  Biochemistry, 47, 12078-12086.
PDB codes: 2vv6 2vv7 2vv8
18568157 R.Chowdhury, A.Hardy, and C.J.Schofield (2008).
The human oxygen sensing machinery and its manipulation.
  Chem Soc Rev, 37, 1308-1319.  
17223691 A.Pandini, M.S.Denison, Y.Song, A.A.Soshilov, and L.Bonati (2007).
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis.
  Biochemistry, 46, 696-708.  
17913493 G.M.Clore, C.Tang, and J.Iwahara (2007).
Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement.
  Curr Opin Struct Biol, 17, 603-616.  
17084097 J.Iwahara, C.Tang, and G.Marius Clore (2007).
Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules.
  J Magn Reson, 184, 185-195.  
17415528 J.W.Kim, P.Gao, and C.V.Dang (2007).
Effects of hypoxia on tumor metabolism.
  Cancer Metastasis Rev, 26, 291-298.  
17250999 T.Mittag, and J.D.Forman-Kay (2007).
Atomic-level characterization of disordered protein ensembles.
  Curr Opin Struct Biol, 17, 3.  
17200735 V.Buttani, A.Losi, T.Eggert, U.Krauss, K.E.Jaeger, Z.Cao, and W.Gärtner (2007).
Conformational analysis of the blue-light sensing protein YtvA reveals a competitive interface for LOV-LOV dimerization and interdomain interactions.
  Photochem Photobiol Sci, 6, 41-49.  
17023418 H.Sekine, J.Mimura, M.Yamamoto, and Y.Fujii-Kuriyama (2006).
Unique and overlapping transcriptional roles of arylhydrocarbon receptor nuclear translocator (Arnt) and Arnt2 in xenobiotic and hypoxic responses.
  J Biol Chem, 281, 37507-37516.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.