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- PDB-7xhv: Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7xhv
TitleCrystal Structure of the NPAS4-ARNT heterodimer in complex with DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')
  • DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
  • Neuronal PAS domain-containing protein 4
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
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 / cellular response to corticosterone stimulus / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex ...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 / cellular response to corticosterone stimulus / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / inhibitory synapse assembly / short-term memory / inhibitory postsynaptic potential / regulation of synaptic transmission, GABAergic / social behavior / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / long-term memory / excitatory postsynaptic potential / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of synaptic plasticity / 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 / postsynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Nuclear translocator / PAS fold-3 / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Nuclear translocator / PAS fold-3 / 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 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Neuronal PAS domain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.996 Å
AuthorsSun, X.N. / Jing, L.Q. / Li, F.W. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZR2021JQ30 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family.
Authors: Sun, X. / Jing, L. / Li, F. / Zhang, M. / Diao, X. / Zhuang, J. / Rastinejad, F. / Wu, D.
History
DepositionApr 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Neuronal PAS domain-containing protein 4
C: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)64,0834
Polymers64,0834
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-81 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.846, 72.846, 272.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1- ...ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1-beta / HIF1-beta


Mass: 30942.221 Da / Num. of mol.: 1 / Fragment: 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 Neuronal PAS domain-containing protein 4 / Neuronal PAS4 / HLH-PAS transcription factor NXF / Limbic-enhanced PAS protein / LE-PAS


Mass: 23343.830 Da / Num. of mol.: 1 / Fragment: NPAS4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas4 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8BGD7
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')


Mass: 5034.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Mass: 4763.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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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: 2.82 Å3/Da / Density % sol: 56.43 % / Mosaicity: 0.924 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: ammonium tartrate dibasic, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: Feb 4, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 3.996→50 Å / Num. obs: 6850 / % possible obs: 99.9 % / Redundancy: 16.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.029 / Rrim(I) all: 0.115 / Χ2: 0.993 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4-4.0715.90.8133380.9260.2060.840.994100
4.07-4.14170.6493100.9340.1580.6691.038100
4.14-4.2216.20.4983280.9650.1250.5141.002100
4.22-4.3116.60.3793470.9820.0920.391.039100
4.31-4.4180.3853110.9690.0920.3961.011100
4.4-4.517.40.3413380.9770.0830.3511.042100
4.5-4.6217.20.2823400.9940.0680.291.016100
4.62-4.7417.30.263230.9870.0630.2681.028100
4.74-4.8816.70.2573390.990.0630.2651.049100
4.88-5.0417.40.2013230.9890.0480.2071.025100
5.04-5.2215.40.1973510.990.050.2041.007100
5.22-5.4316.20.1823330.9920.0460.1880.987100
5.43-5.6715.60.163370.9930.0410.1650.963100
5.67-5.9717.70.1493390.9960.0350.1530.983100
5.97-6.3516.90.1463440.9940.0360.1510.982100
6.35-6.8416.30.1323460.9930.0330.1360.923100
6.84-7.5215.80.0933510.9980.0230.0960.92100
7.52-8.614.40.0693670.9980.0180.0710.904100
8.6-10.8215.90.0583670.9980.0150.060.83499.7
10.82-5012.30.0664180.9980.0190.0691.13199.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 3.996→31.074 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3306 305 4.51 %
Rwork0.2725 6458 -
obs0.2751 6763 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.61 Å2 / Biso mean: 57.8606 Å2 / Biso min: 29.53 Å2
Refinement stepCycle: final / Resolution: 3.996→31.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 656 0 0 3540
Num. residues----401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.9964-5.03150.31991430.27613127
5.0315-31.0740.34291620.26823331

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