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- PDB-6x21: Crystal structure of PT1673 bound to HIF2a-B*:ARNT-B* complex -

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Basic information

Entry
Database: PDB / ID: 6x21
TitleCrystal structure of PT1673 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 / 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 / visual perception / regulation of heart rate / positive regulation of erythrocyte differentiation / 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 / 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
Similarity search - Domain/homology
Chem-UKJ / 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: 1.54 Å
AuthorsDu, X.
CitationJournal: To Be Published
Title: Crystal structure of PT1673 bound to HIF2a-B*:ARNT-B* complex
Authors: Du, X.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)27,6203
Polymers27,1942
Non-polymers4261
Water1,58588
1
A: Endothelial PAS domain-containing protein 1
hetero molecules

B: Aryl hydrocarbon receptor nuclear translocator


Theoretical massNumber of molelcules
Total (without water)27,6203
Polymers27,1942
Non-polymers4261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x+1/2,y-1/2,-z-11
Buried area1630 Å2
ΔGint-10 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.793, 83.504, 41.373
Angle α, β, γ (deg.)90.000, 106.780, 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: 13295.017 Da / Num. of mol.: 1 / Mutation: R247E
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: 13898.778 Da / Num. of mol.: 1 / Mutation: E362R
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-UKJ / 1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene


Mass: 426.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H7BrF3NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: Bis-Tris, pH5.4, 16% PEG3350 / Temp details: IN AN INCUBATOR

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen vapor / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9715 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 38676 / % possible obs: 92.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Χ2: 1.378 / Net I/σ(I): 11.2 / Num. measured all: 134679
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.54-1.5730.93918910.861191.2
1.57-1.613.30.7719970.825196.7
1.61-1.643.60.74220440.931197.8
1.64-1.693.70.58520280.91198.3
1.69-1.733.70.42920350.947198.4
1.73-1.783.70.34720490.985198.4
1.78-1.843.70.27420600.999198.7
1.84-1.913.70.19620471.101198.7
1.91-1.983.70.14820661.17198.9
1.98-2.073.70.10820581.354199.1
2.07-2.183.70.08520611.543199.3
2.18-2.323.70.07220831.579199.2
2.32-2.53.70.06120431.807199.3
2.5-2.753.60.05520962.137199.7
2.75-3.153.60.04920892.566199.7
3.15-3.963.40.03220842.282199.5
3.96-503.60.02620571.816196.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D0C

6d0c


Resolution: 1.54→26.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.708 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 1733 5 %RANDOM
Rwork0.2046 ---
obs0.206 33105 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.96 Å2 / Biso mean: 23.091 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-0.34 Å2
2---0.54 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.54→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 0 88 1848
Biso mean---29.85 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021836
X-RAY DIFFRACTIONr_angle_refined_deg2.3981.9442480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57424.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6221510
X-RAY DIFFRACTIONr_chiral_restr0.1640.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021397
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 117 -
Rwork0.323 2233 -
all-2350 -
obs--92.16 %

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