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- PDB-3f1p: Crystal structure of a high affinity heterodimer of HIF2 alpha an... -

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Basic information

Entry
Database: PDB / ID: 3f1p
TitleCrystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains
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 / visual perception / NPAS4 regulates expression of target genes / Pexophagy / 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 / response to oxidative stress / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / 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 / 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) / 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
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: 1.17 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_sheet
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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7812
Polymers27,7812
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.916, 82.565, 41.032
Angle α, β, γ (deg.)90.00, 106.02, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion combined with microseeding / pH: 6.5
Details: 30% PEG3350, 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: 0.97904 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007
RadiationMonochromator: Custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.17→26.93 Å / Num. obs: 76140 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 11.46 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.2
Reflection shellResolution: 1.17→1.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1679 / % possible all: 64.3

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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: 1.17→26.926 Å / SU ML: 0.12 / Isotropic thermal model: individual anisotropic B values / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1665 1523 2.01 %random
Rwork0.1407 ---
obs0.1412 75655 95.14 %-
all-76140 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.809 Å2 / ksol: 0.429 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.9921 Å2-0 Å20.7563 Å2
2---1.6678 Å20 Å2
3----0.3244 Å2
Refinement stepCycle: LAST / Resolution: 1.17→26.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 0 263 4275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_deg1.368
X-RAY DIFFRACTIONf_improper_angle_d0.136
X-RAY DIFFRACTIONf_dihedral_angle_d16.02
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 (%)
1.17-1.20780.21961040.17964988509270
1.2078-1.25090.20611450.16856585673094
1.2509-1.3010.19891180.14376810692896
1.301-1.36020.17481260.13026881700797
1.3602-1.4320.14211390.12326814695397
1.432-1.52170.13581600.11896884704497
1.5217-1.63910.15451180.10946940705898
1.6391-1.80410.13811540.11276935708998
1.8041-2.0650.17871380.12167056719499
2.065-2.60140.15391410.13471047245100
2.6014-26.93360.16921800.159971357315100

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