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- PDB-3f1n: Crystal structure of a high affinity heterodimer of HIF2 alpha an... -

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Basic information

Entry
Database: PDB / ID: 3f1n
TitleCrystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with internally bound ethylene glycol.
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 / blood vessel remodeling / embryonic placenta development / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / regulation of heart rate / positive regulation of erythrocyte differentiation / visual perception / positive regulation of glycolytic process / Pexophagy / erythrocyte differentiation / mitochondrion organization / 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 / negative regulation of inflammatory response / multicellular organismal-level iron ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Neddylation / 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 / transcription regulator complex / sequence-specific DNA binding / response to oxidative stress / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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) ...: / 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 / Beta-Lactamase / 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.479 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 / 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 1.4Sep 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)27,9685
Polymers27,7812
Non-polymers1863
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint0 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.321, 82.908, 41.400
Angle α, β, γ (deg.)90.00, 106.08, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
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-ID / Wavelength: 0.97924 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 13, 2007
RadiationMonochromator: Custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.48→31 Å / Num. all: 39281 / Num. obs: 39281 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 17.72 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 32.6
Reflection shellResolution: 1.48→1.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 1.9 / Num. unique all: 933 / % possible all: 91.3

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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: 1.479→30.972 Å / SU ML: 0.19 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 1.37 / 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 (PDB entry 3F1P) and is modeled with a ...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 (PDB entry 3F1P) and is modeled with a heavy weighting toward geometric ideality at the expense of a best fit against poor density.
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 1972 5.02 %random
Rwork0.1716 ---
obs0.173 39277 98.87 %-
all-39281 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.873 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.4438 Å2-0 Å22.8903 Å2
2---2.095 Å20 Å2
3----2.3488 Å2
Refinement stepCycle: LAST / Resolution: 1.479→30.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 30 180 4010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_deg1.226
X-RAY DIFFRACTIONf_improper_angle_d0.097
X-RAY DIFFRACTIONf_dihedral_angle_d15.348
X-RAY DIFFRACTIONf_planarity_d0.007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4786-1.51550.30621210.23582392251389
1.5155-1.55650.251390.20952597273696
1.5565-1.60230.21441470.19132692283999
1.6023-1.6540.21711330.180226932826100
1.654-1.71310.20571270.168826932820100
1.7131-1.78170.21331290.161627092838100
1.7817-1.86280.21651370.163926672804100
1.8628-1.9610.19041660.157326842850100
1.961-2.08380.18861500.154926682818100
2.0838-2.24470.18181370.157626952832100
2.2447-2.47050.1831340.16626962830100
2.4705-2.82780.20131540.163826972851100
2.8278-3.56190.18971510.162627022853100
3.5619-30.97870.19361470.17992720286799
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)
1-0.09520.22830.12733.13260.19011.1347-0.00450.0563-0.0087-0.0544-0.0225-0.1508-0.0450.00860.01910.0847-0.0236-0.00280.133-0.01690.12416.0853-43.29519.6691
20.4105-0.2266-0.07540.54420.46751.14430.0486-0.02290.01660.02390.0262-0.0112-0.0215-0.056-0.06660.06930.01090.00680.05790.0210.066218.1967-18.955418.0326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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