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- PDB-7v7l: Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex -

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Basic information

Entry
Database: PDB / ID: 7v7l
TitleCrystal Structure of the Heterodimeric HIF-3a:ARNT Complex
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Hypoxia-inducible factor 3-alpha
KeywordsTRANSCRIPTION / Hypoxia-inducible factor / bHLH-PAS
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 / response to toxic substance / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / 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 / DNA-binding transcription factor activity / protein heterodimerization 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
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: 2.3 Å
AuthorsDiao, X. / Ren, X. / Li, F.W. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,3842
Polymers81,3842
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-66 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.843, 86.291, 143.701
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
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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
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: Jan 15, 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: 2.299→50 Å / Num. obs: 48740 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.975 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3411.81.09618320.7690.3261.1450.95798.7
2.34-2.3812.50.99118020.8120.2861.0320.97699.7
2.38-2.43130.80918280.8740.2310.8420.96299.6
2.43-2.48130.68318500.9120.1950.7110.97699.9
2.48-2.5312.50.59818310.9210.1750.6241100
2.53-2.5912.30.50518060.9390.1490.5271.015100
2.59-2.6613.60.43718540.960.1210.4541100
2.66-2.7313.60.35418440.9710.0990.3671.007100
2.73-2.8113.50.28818210.9830.080.2990.996100
2.81-2.913.40.22318480.9890.0630.2311.01100
2.9-313.10.18518750.9910.0520.1921.013100
3-3.1212.40.14118420.9940.0420.1481.011100
3.12-3.2613.20.11118320.9960.0310.1151.03699.9
3.26-3.4413.70.08618650.9980.0240.091.041100
3.44-3.6513.50.06518700.9990.0180.0681.048100
3.65-3.9313.20.05318710.9990.0150.0551.026100
3.93-4.3312.50.04218810.9990.0120.0440.97999.8
4.33-4.9513.60.03818890.9990.0110.040.955100
4.95-6.2412.40.03719210.9990.0110.0380.76899.9
6.24-5012.20.03203610.0090.0320.71399.6

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZP4

4zp4


Resolution: 2.3→36.989 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 2695 5.53 %
Rwork0.204 46045 -
obs0.2063 48740 69.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.51 Å2 / Biso mean: 46.5642 Å2 / Biso min: 13.69 Å2
Refinement stepCycle: final / Resolution: 2.3→36.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 0 275 4871
Biso mean---43.43 -
Num. residues----579
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34070.3356840.3007145741
2.3407-2.38570.3925950.2896163147
2.3857-2.43440.36191020.2779176350
2.4344-2.48740.29311020.2737175051
2.4874-2.54520.36981070.2837185352
2.5452-2.60880.32561050.2779180252
2.6088-2.67940.32741070.2743183452
2.6794-2.75820.3271060.2803183252
2.7582-2.84720.35661050.2694183553
2.8472-2.94890.30481110.2767187853
2.9489-3.06690.2851140.2521195556
3.0669-3.20640.27311400.2168244169
3.2064-3.37540.26791890.2032316191
3.3754-3.58670.22692020.1913343298
3.5867-3.86330.22722030.16783507100
3.8633-4.25160.19952030.163467100
4.2516-4.86560.20882060.15073505100
4.8656-6.12570.22862110.19413482100
6.1257-36.9890.19762030.2143346099
Refinement TLS params.Method: refined / Origin x: 30.6786 Å / Origin y: 2.4185 Å / Origin z: 17.9708 Å
111213212223313233
T0.1543 Å2-0.0228 Å2-0.0621 Å2-0.1613 Å2-0.0115 Å2--0.2246 Å2
L0.8183 °2-0.5515 °20.2905 °2-0.7063 °2-0.6099 °2--1.0674 °2
S0.0436 Å °0.1254 Å °-0.059 Å °-0.0615 Å °0.021 Å °0.011 Å °0.0996 Å °0.113 Å °-0.0473 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA98 - 464
2X-RAY DIFFRACTION1allB19 - 358
3X-RAY DIFFRACTION1allS1 - 318

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