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- PDB-2a24: HADDOCK Structure of HIF-2a/ARNT PAS-B Heterodimer -

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Basic information

Entry
Database: PDB / ID: 2a24
TitleHADDOCK Structure of HIF-2a/ARNT PAS-B Heterodimer
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain protein 1
KeywordsTRANSCRIPTION / ARNT / HIF / hypoxia / PAS
Function / homology
Function and homology information


myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / epithelial cell maturation / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / blood vessel remodeling / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / Pexophagy / NPAS4 regulates expression of target genes / visual perception / positive regulation of endothelial cell proliferation / regulation of heart rate / mitochondrion organization / positive regulation of glycolytic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / transcription coactivator binding / PPARA activates gene expression / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / Neddylation / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / response to oxidative stress / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain ...HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCard, P.B. / Erbel, P.J. / Gardner, K.H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization.
Authors: Card, P.B. / Erbel, P.J. / Gardner, K.H.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothelial PAS domain protein 1
B: Aryl hydrocarbon receptor nuclear translocator


Theoretical massNumber of molelcules
Total (without water)25,3122
Polymers25,3122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50
RepresentativeModel #1lowest energy

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Components

#1: Protein Endothelial PAS domain protein 1 / EPAS-1 / Member of PAS protein 2 / MOP2 / Hypoxia-inducible factor 2 alpha / HIF-2 alpha / HIF2 ...EPAS-1 / Member of PAS protein 2 / MOP2 / Hypoxia-inducible factor 2 alpha / HIF-2 alpha / HIF2 alpha / HIF-1 alpha-like factor / HLF


Mass: 12488.202 Da / Num. of mol.: 1 / Fragment: C-terminal PAS domain (PAS-B) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99814
#2: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1 beta / HIF-1 beta


Mass: 12823.554 Da / Num. of mol.: 1 / Fragment: C-terminal PAS domain (PAS-B) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27540

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N/1H HSQC
12215N/1H HSQC
NMR detailsText: 15N/1H HSQC was used to Monitor chemical shift perturbation upon complex formation to identify interaction interface.

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Sample preparation

Details
Solution-IDContents
1250 micro M (15N)HIF-2alpha PAS-B (240-350) + 1mM ARNT PAS-B (356-470), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT
2250 micro M (15N)ARNT PAS-B (356-470) + 1mM HIF-2alpha PAS-B (240-350), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT
Sample conditionsIonic strength: 50mM Tris, 17mM NaCl, 5mM DTT / pH: 7.5 / Temperature units: K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.2BONVINstructure solution
NMRPipe2.3DELAGLIOprocessing
CNS1.1BRUNGERstructure solution
NMRView5.2.2JOHNSONdata analysis
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 50 / Conformers submitted total number: 20

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