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- PDB-3h7w: Crystal structure of the high affinity heterodimer of HIF2 alpha ... -

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Basic information

Entry
Database: PDB / ID: 3h7w
TitleCrystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS017
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 / positive regulation of hormone biosynthetic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / regulation of protein neddylation / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / regulation of protein neddylation / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / Phase I - Functionalization of compounds / epithelial cell maturation / 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 / blood vessel remodeling / Endogenous sterols / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / visual perception / regulation of heart rate / lung development / positive regulation of erythrocyte differentiation / Pexophagy / positive regulation of glycolytic process / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / mRNA transcription by RNA polymerase II / PPARA activates gene expression / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / transcription coactivator binding / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Neddylation / response to oxidative stress / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / cellular response to hypoxia / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / cell differentiation / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / 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 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif ...HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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-018 / Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0843
Polymers27,7812
Non-polymers3021
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.890, 82.727, 41.158
Angle α, β, γ (deg.)90.00, 106.48, 90.00
Int Tables number5
Space group name H-MC121
Detailsto generate the biologically relevant complex, the symmetry operator (1/2-x,y-1/2,1-z) should applied to chain B.

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Components

#1: 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
#2: 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
#3: Chemical ChemComp-018 / 2-nitro-N-(thiophen-3-ylmethyl)-4-(trifluoromethyl)aniline


Mass: 302.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F3N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M BisTris, 17% PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING 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: 1.65→40 Å / Num. all: 28092 / Num. obs: 28092 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1354 / % possible all: 95.2

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Processing

Software
NameClassification
HKL-3000data collection
REFMACrefinement
HKL-3000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3f1p

3f1p


Resolution: 1.65→22.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.094 / SU ML: 0.073 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 1409 5 %RANDOM
Rwork0.19715 ---
all0.19907 28092 --
obs0.19907 28092 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.486 Å2
Refine analyzeLuzzati coordinate error obs: 0.2024 Å
Refinement stepCycle: LAST / Resolution: 1.65→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 20 182 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221913
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9432594
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1292495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0841511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021466
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21334
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0271.51167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58821840
X-RAY DIFFRACTIONr_scbond_it2.4523875
X-RAY DIFFRACTIONr_scangle_it3.5594.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 103 -
Rwork0.298 1827 -
obs-1354 95.2 %

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