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- PDB-1p97: NMR structure of the C-terminal PAS domain of HIF2a -

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Basic information

Entry
Database: PDB / ID: 1p97
TitleNMR structure of the C-terminal PAS domain of HIF2a
ComponentsEndothelial PAS domain protein 1
KeywordsTRANSCRIPTION / Mixed alpha-beta fold
Function / homology
Function and homology information


myoblast fate commitment / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / embryonic placenta development ...myoblast fate commitment / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / embryonic placenta development / blood vessel remodeling / visual perception / Pexophagy / regulation of heart rate / mitochondrion organization / 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 / multicellular organismal-level iron ion homeostasis / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytosol
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 / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS 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 / 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
Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsErbel, P.J. / Card, P.B. / Karakuzu, O. / Bruick, R.K. / Gardner, K.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural basis for PAS domain heterodimerization in the basic helix-loop-helix-PAS transcription factor hypoxia-inducible factor.
Authors: Erbel, P.J. / Card, P.B. / Karakuzu, O. / Bruick, R.K. / Gardner, K.H.
History
DepositionMay 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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


Theoretical massNumber of molelcules
Total (without water)13,1931
Polymers13,1931
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 / 1000structures with the lowest energy
Representative

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Components

#1: Protein Endothelial PAS domain protein 1 / EPAS-1 / Member of PAS protein 2 / MOP2


Mass: 13192.977 Da / Num. of mol.: 1 / Fragment: C-terminal PAS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1 / Plasmid: pGb1-parallel / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99814

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY

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Sample preparation

DetailsContents: 0.9mM HIF2a (240-350) U-15N,13C; 50 mM Tris buffer, 15 mM NaCl, 5 mM DTT (pH 7.3); 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 15 mM - 75 mM / pH: 7.3 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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