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- PDB-5sy7: Crystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA -

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Basic information

Entry
Database: PDB / ID: 5sy7
TitleCrystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
  • Neuronal PAS domain-containing protein 3
Keywordstranscription/DNA / bHLH-PAS protein / transcription factor / heterodimeric complex / transcription-DNA complex
Function / homology
Function and homology information


Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / positive regulation of protein sumoylation / maternal behavior ...Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / positive regulation of protein sumoylation / maternal behavior / startle response / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / locomotory behavior / negative regulation of inflammatory response / response to toxic substance / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / 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 / 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 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 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
DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Neuronal PAS domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsWu, D. / Su, X. / Potluri, N. / Kim, Y. / Rastinejad, F.
CitationJournal: Elife / Year: 2016
Title: NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors.
Authors: Wu, D. / Su, X. / Potluri, N. / Kim, Y. / Rastinejad, F.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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 3
C: DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
D: DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)102,5534
Polymers102,5534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-86 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.831, 64.831, 249.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 43437.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53762
#2: Protein Neuronal PAS domain-containing protein 3 / Neuronal PAS3 / Basic-helix-loop-helix-PAS protein MOP6 / Member of PAS protein 6


Mass: 46225.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas3, Mop6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QZQ0
#3: DNA chain DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')


Mass: 6527.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA sense strand / Source: (synth.) Mus musculus (house mouse)
#4: DNA chain DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Mass: 6363.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA antisense strand / Source: (synth.) Mus musculus (house mouse)

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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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM NH4F, 9% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 7195 / % possible obs: 94.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 37.41 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 20.01 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
4.2-4.273.90.8480.893172.3
4.27-4.354.30.6120.895169.9
4.35-4.434.30.5460.853183.3
4.43-4.524.30.4490.971187.6
4.52-4.624.40.3990.968192.5
4.62-4.734.80.4140.97196.4
4.73-4.855.20.4360.966197.4
4.85-4.985.30.3350.9761100
4.98-5.135.50.340.9831100
5.13-5.295.60.2770.9841100
5.29-5.485.50.2790.965199.7
5.48-5.75.80.2160.9811100
5.7-5.965.50.1850.977199.7
5.96-6.275.60.1480.9891100
6.27-6.665.50.1180.983199.7
6.66-7.185.50.0870.985199.7
7.18-7.95.40.0610.992199.7
7.9-9.035.30.0480.988199.7
9.03-11.365.40.0430.995199.7
11.36-505.10.0450.982193.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 4.2→45.842 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.3614 276 4.7 %
Rwork0.2719 --
obs0.2763 5868 77.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.01 Å2 / Biso mean: 66.8626 Å2 / Biso min: 5.11 Å2
Refinement stepCycle: final / Resolution: 4.2→45.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 855 0 0 5313
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045501
X-RAY DIFFRACTIONf_angle_d0.7317595
X-RAY DIFFRACTIONf_chiral_restr0.045851
X-RAY DIFFRACTIONf_plane_restr0.005816
X-RAY DIFFRACTIONf_dihedral_angle_d17.5393140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.1881-5.27530.34771110.27132009212056
5.2753-45.84520.37131650.27223583374899

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