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- PDB-7v7w: Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex with o... -

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Basic information

Entry
Database: PDB / ID: 7v7w
TitleCrystal Structure of the Heterodimeric HIF-3a:ARNT Complex with oleoylethanolamide (OEA)
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Hypoxia-inducible factor 3-alpha
KeywordsTRANSCRIPTION / Hypoxia-inducible factor
Function / homology
Function and homology information


Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / Neddylation ...Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / Neddylation / positive regulation of protein sumoylation / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of glycolytic process / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / response to toxic substance / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / angiogenesis / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / protein dimerization activity / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / apoptotic process / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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 ...: / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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
(Z)-N-(2-hydroxyethyl)octadec-9-enamide / Aryl hydrocarbon receptor nuclear translocator / Hypoxia-inducible factor 3-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.507 Å
AuthorsDiao, X. / Ren, X. / Li, F.W. / Zhang, M. / Sun, X. / Wu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177063 China
CitationJournal: Nat Commun / Year: 2022
Title: Identification of oleoylethanolamide as an endogenous ligand for HIF-3 alpha.
Authors: Diao, X. / Ye, F. / Zhang, M. / Ren, X. / Tian, X. / Lu, J. / Sun, X. / Hou, Z. / Chen, X. / Li, F. / Zhuang, J. / Ding, H. / Peng, C. / Rastinejad, F. / Luo, C. / Wu, D.
History
DepositionAug 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Hypoxia-inducible factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7103
Polymers81,3842
Non-polymers3261
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-59 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.944, 86.787, 143.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein


Mass: 40683.133 Da / Num. of mol.: 1 / Fragment: Hydrocarbon receptor nuclear translocator ARNT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53762
#2: Protein Hypoxia-inducible factor 3-alpha / HIF-3-alpha / HIF3-alpha


Mass: 40701.211 Da / Num. of mol.: 1 / Fragment: Hypoxia-inducible factor 3, HIF-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hif3a / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0VBL6
#3: Chemical ChemComp-5YM / (Z)-N-(2-hydroxyethyl)octadec-9-enamide


Mass: 325.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H39NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium citrate tribasic dihydrate, 2-Propanol, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2019 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28966 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.095 / Χ2: 0.996 / Net I/σ(I): 6.7 / Num. measured all: 313133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5410.81.23114380.7190.3881.2920.942100
2.54-2.59111.01713930.7810.3181.0660.943100
2.59-2.6410.70.92514460.7760.2930.9710.979100
2.64-2.6910.70.73714170.8440.2340.7740.97299.9
2.69-2.7510.20.64914270.8670.2120.6840.97100
2.75-2.829.90.48714250.9110.1620.5140.974100
2.82-2.8911.10.41114260.9570.1270.4310.978100
2.89-2.9611.40.33614240.9690.1030.3520.976100
2.96-3.0511.30.28314260.9780.0870.2961.005100
3.05-3.1511.20.20514400.9880.0630.2151.01499.9
3.15-3.2611.30.1814450.990.0560.1891.052100
3.26-3.3911.10.13914260.9940.0430.1461.035100
3.39-3.5510.70.10214490.9950.0330.1071.01100
3.55-3.73100.08514460.9960.0280.091.05299.6
3.73-3.9711.50.07714310.9970.0240.0811.058100
3.97-4.2711.30.06614710.9980.020.0691.061100
4.27-4.711.10.0614650.9980.0190.0631.07399.9
4.7-5.3810.10.05714820.9970.0190.060.96599.5
5.38-6.7810.90.05814970.9980.0180.0610.936100
6.78-509.80.04915920.9980.0160.0520.91899.3

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V7L

7v7l


Resolution: 2.507→35.929 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1997 7.15 %
Rwork0.2178 25937 -
obs0.2208 27934 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.08 Å2 / Biso mean: 50.3906 Å2 / Biso min: 16.51 Å2
Refinement stepCycle: final / Resolution: 2.507→35.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 23 149 4686
Biso mean--51.02 47.35 -
Num. residues----567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5075-2.57020.2921990.2753128368
2.5702-2.63960.29641260.2804163886
2.6396-2.71730.30191430.2695184197
2.7173-2.8050.30841430.2576185998
2.805-2.90520.26581460.24821896100
2.9052-3.02140.33041460.24871896100
3.0214-3.15890.29871480.24221915100
3.1589-3.32530.28091470.23241910100
3.3253-3.53350.27421470.21691909100
3.5335-3.8060.25551470.20051910100
3.806-4.18850.2421490.19271942100
4.1885-4.79340.17761500.1651947100
4.7934-6.03450.22261510.20441963100
6.0345-35.9290.28671550.226202898
Refinement TLS params.Method: refined / Origin x: 30.3161 Å / Origin y: 2.7462 Å / Origin z: 17.5073 Å
111213212223313233
T0.1964 Å2-0.0308 Å2-0.0435 Å2-0.205 Å2-0.001 Å2--0.2711 Å2
L1.1772 °2-0.5795 °20.8027 °2-0.9921 °2-0.7274 °2--1.6761 °2
S0.0658 Å °0.1881 Å °-0.158 Å °0.0062 Å °0.069 Å °-0.0304 Å °0.1229 Å °0.1711 Å °-0.0973 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA99 - 464
2X-RAY DIFFRACTION1allB19 - 357
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 158
5X-RAY DIFFRACTION1allS160 - 191

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