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- PDB-3h82: Crystal structure of the high affinity heterodimer of HIF2 alpha ... -

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Basic information

Entry
Database: PDB / ID: 3h82
TitleCrystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS020
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsTRANSCRIPTION / PAS domain / heterodimer / protein ligand complex. / Activator / Angiogenesis / Congenital erythrocytosis / Developmental protein / Differentiation / Disease mutation / DNA-binding / Hydroxylation / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation / Alternative splicing / Polymorphism
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 / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / epithelial cell maturation / 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 / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / visual perception / Pexophagy / positive regulation of glycolytic process / regulation of heart rate / mitochondrion organization / 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 / PPARA activates gene expression / transcription coactivator binding / 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 / Neddylation / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / 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 / 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
Chem-020 / Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKey, J.M. / Scheuermann, T.H. / Anderson, P.C. / Daggett, V. / Gardner, K.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B
Authors: Key, J. / Scheuermann, T.H. / Anderson, P.C. / Daggett, V. / Gardner, K.H.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Aryl hydrocarbon receptor nuclear translocator
A: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0683
Polymers27,7812
Non-polymers2861
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-10 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.889, 70.280, 42.348
Angle α, β, γ (deg.)90.00, 108.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biologically relevant complex is present in the ASU

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1 beta / HIF-1 beta


Mass: 14243.098 Da / Num. of mol.: 1
Fragment: ARNT C-terminal PAS domain (UNP residues 356 to 470)
Mutation: E362R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ARNT, Aryl Hydrocarbon Receptor Nuclear Translocator, BHLHE2
Plasmid: phis-GB1-ARNT-PAS-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27540
#2: Protein Endothelial PAS domain-containing protein 1 / EPAS-1 / Member of PAS protein 2 / Basic-helix-loop-helix-PAS protein MOP2 / Hypoxia-inducible ...EPAS-1 / Member of PAS protein 2 / Basic-helix-loop-helix-PAS protein MOP2 / Hypoxia-inducible factor 2 alpha / HIF-2 alpha / HIF2 alpha / HIF-1 alpha-like factor / HLF


Mass: 13538.300 Da / Num. of mol.: 1
Fragment: HIF2alpha C-terminal PAS domain (UNP residues 239 to 350)
Mutation: R247E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1, HIF2A, Hypoxia Inducible Factor 2 alpha, MOP2 / Plasmid: phis-GB1-HIF2aPAS-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99814
#3: Chemical ChemComp-020 / N-(furan-2-ylmethyl)-2-nitro-4-(trifluoromethyl)aniline


Mass: 286.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F3N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M BisTris, 25% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 34380 / Num. obs: 34380 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.48 / Num. unique all: 1241 / % possible all: 68.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F1N

3f1n


Resolution: 1.5→26.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.686 / SU ML: 0.064 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23388 1710 5 %RANDOM
Rwork0.19436 ---
all0.1964 34380 --
obs0.1964 34380 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refine analyzeLuzzati coordinate error obs: 0.1815 Å
Refinement stepCycle: LAST / Resolution: 1.5→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 20 215 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212038
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9422773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75524.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.261512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021591
X-RAY DIFFRACTIONr_nbd_refined0.2440.2931
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.225
X-RAY DIFFRACTIONr_mcbond_it1.3411.51246
X-RAY DIFFRACTIONr_mcangle_it2.07121989
X-RAY DIFFRACTIONr_scbond_it2.9983913
X-RAY DIFFRACTIONr_scangle_it4.2214.5784
LS refinement shellResolution: 1.5→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 96 -
Rwork0.297 1764 -
obs-1241 68.8 %

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