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- PDB-3f1o: Crystal structure of the high affinity heterodimer of HIF2 alpha ... -

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Basic information

Entry
Database: PDB / ID: 3f1o
TitleCrystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with an internally-bound artificial ligand
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsTRANSCRIPTION / PAS domain / heterodimer / internal cavity / 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 / Pexophagy / visual perception / regulation of heart rate / positive regulation of glycolytic process / 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 / sequence-specific DNA binding / transcription regulator complex / 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-2XY / 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: 1.598 Å
AuthorsScheuermann, T.H. / Tomchick, D.R. / Machius, M. / Guo, Y. / Bruick, R.K. / Gardner, K.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.
Authors: Scheuermann, T.H. / Tomchick, D.R. / Machius, M. / Guo, Y. / Bruick, R.K. / Gardner, K.H.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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)28,1354
Polymers27,7812
Non-polymers3532
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-6 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.761, 83.019, 41.553
Angle α, β, γ (deg.)90.00, 106.36, 90.00
Int Tables number5
Space group name H-MC121

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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: HIF2 alpha C-terminal PAS domain / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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: 14243.098 Da / Num. of mol.: 1 / Fragment: ARNT C-terminal PAS domain / Mutation: E362R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, Aryl Hydrocarbon Receptor Nuclear Translocator / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P27540
#3: Chemical ChemComp-2XY / N-[2-nitro-4-(trifluoromethyl)phenyl]morpholin-4-amine


Mass: 291.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12F3N3O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion combined with microseeding / pH: 6.5
Details: 30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT , pH 6.5, vapor diffusion combined with microseeding, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 22, 2007
RadiationMonochromator: Custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→26.93 Å / Num. all: 31184 / Num. obs: 31184 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.93 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.5
Reflection shellResolution: 1.6→1.61 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.1 / Num. unique all: 732 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.3refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B02

2b02


Resolution: 1.598→26.93 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
Details: The density for the N463 side chain is relatively poor, that its conformation was informed by that observed in the higher resolution apo structure (rcsb050035, 3F1P) and modeled with a heavy ...Details: The density for the N463 side chain is relatively poor, that its conformation was informed by that observed in the higher resolution apo structure (rcsb050035, 3F1P) and modeled with a heavy weighting toward geometric ideality at the expense of a best fit against poor density
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1581 5.07 %random
Rwork0.1663 ---
obs0.1683 31173 98.08 %-
all-31184 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.905 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-4.4362 Å2-0 Å21.3278 Å2
2---1.3044 Å20 Å2
3----3.1318 Å2
Refinement stepCycle: LAST / Resolution: 1.598→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 30 186 4074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.048
X-RAY DIFFRACTIONf_improper_angle_d0.081
X-RAY DIFFRACTIONf_dihedral_angle_d15.451
X-RAY DIFFRACTIONf_planarity_d0.009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5978-1.64930.23681360.20212541267794
1.6493-1.70830.2411390.18082688282798
1.7083-1.77670.20411230.16492671279498
1.7767-1.85750.20891220.16662716283898
1.8575-1.95540.17751400.15272662280298
1.9554-2.07790.20741510.15412708285998
2.0779-2.23820.18621260.14932726285299
2.2382-2.46330.17741490.16012705285499
2.4633-2.81950.19331660.15632700286699
2.8195-3.55090.18881630.16132717288099
3.5509-26.93360.21581660.17242758292499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.17870.3048-0.07431.6670.22940.4414-0.02470.0086-0.0198-0.12770.0096-0.0448-0.06030.03540.00870.1114-0.0102-0.00890.1308-0.01310.134916.0554-43.57479.9701
20.2044-0.1221-0.01860.39090.37250.99820.0351-0.03880.01430.02510.03030.0052-0.0365-0.0231-0.0540.09130.0050.0050.08060.01180.086618.4012-18.926417.9199
32.7418-0.99011.0945-0.14410.27960.76160.02390.0355-0.0033-0.00760.08870.2030.0025-0.0569-0.10680.16990.03020.01790.20080.04560.205512.1537-41.598110.2748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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