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- PDB-6d09: Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex -

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Basic information

Entry
Database: PDB / ID: 6d09
TitleCrystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsTRANSCRIPTION / Hif2a / Pas B domain / ARNT / hypoxia inducible factor / EPAS1
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 / regulation of protein neddylation / PTK6 Expression / 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 / regulation of protein neddylation / PTK6 Expression / 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 / NPAS4 regulates expression of target genes / positive regulation of endothelial cell proliferation / visual perception / regulation of heart rate / Pexophagy / lung development / positive regulation of erythrocyte differentiation / 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 / transcription coactivator binding / 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 / response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / cellular response to hypoxia / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / 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 / cytoplasm / cytosol
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-FOJ / 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: 1.85 Å
AuthorsDu, X.
CitationJournal: To Be Published
Title: Crystal structure of PT1940 bound to HIF2a-B*:ARNT-B* complex
Authors: Du, X.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1873
Polymers27,7812
Non-polymers4051
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-0 kcal/mol
Surface area11700 Å2
2
A: Endothelial PAS domain-containing protein 1
hetero molecules

B: Aryl hydrocarbon receptor nuclear translocator


Theoretical massNumber of molelcules
Total (without water)28,1873
Polymers27,7812
Non-polymers4051
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x+1/2,y-1/2,-z-11
Buried area1720 Å2
ΔGint-8 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.216, 83.832, 41.410
Angle α, β, γ (deg.)90.000, 106.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endothelial PAS domain-containing protein 1 / EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / ...EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / bHLHe73 / HIF-1-alpha-like factor / HLF / Hypoxia-inducible factor 2-alpha / HIF2-alpha / Member of PAS protein 2 / PAS domain-containing protein 2


Mass: 13538.300 Da / Num. of mol.: 1 / Fragment: residues 239-350 / Mutation: R14E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1, BHLHE73, HIF2A, MOP2, PASD2 / Production host: Escherichia coli (E. coli) / 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 / HIF1-beta


Mass: 14243.098 Da / Num. of mol.: 1 / Fragment: residues 356-470 / Mutation: E13R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27540
#3: Chemical ChemComp-FOJ / 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile


Mass: 405.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8F5NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 50 mM Bis-Tris pH5.4 and 16% PEG3350. Seeding with crushed crystals right after setup

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogrn vapor
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 20464 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Χ2: 1.186 / Net I/σ(I): 20.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2004 / CC1/2: 0.454 / Rpim(I) all: 0.762 / Χ2: 0.921 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-3000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XT2

4xt2


Resolution: 1.85→28.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.629 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 1013 4.9 %RANDOM
Rwork0.2265 ---
obs0.2293 19456 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.32 Å2 / Biso mean: 35.906 Å2 / Biso min: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å2-0.31 Å2
2---1.14 Å20 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 1.85→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 27 21 1828
Biso mean--31.63 35.28 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021873
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9492538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5425218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38524.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9715321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9441510
X-RAY DIFFRACTIONr_chiral_restr0.1720.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211430
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 66 -
Rwork0.345 1370 -
all-1436 -
obs--98.15 %

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