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- PDB-7xi3: Crystal Structure of the NPAS4-ARNT2 heterodimer in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7xi3
TitleCrystal Structure of the NPAS4-ARNT2 heterodimer in complex with DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator 2
  • 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 protein 4
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


nervous system development / cell differentiation / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleoplasm
Similarity search - Function
: / NPAS4 bHLH domain / PAS fold-3 / PAS fold / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Neuronal PAS domain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.274 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 11, 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 2
B: Neuronal PAS domain 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)92,3234
Polymers92,3234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-82 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.773, 72.773, 415.269
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 2


Mass: 44215.363 Da / Num. of mol.: 1 / Fragment: ARNT2
Source method: isolated from a genetically manipulated source
Details: AUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS OK136250 FOR THIS POLYMER.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt2 / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein Neuronal PAS domain protein 4


Mass: 38310.688 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: A1L327
#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: 2.98 Å3/Da / Density % sol: 58.69 % / Mosaicity: 0.706 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: sodium citrate tribasic, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: Jul 18, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 4.274→50 Å / Num. obs: 8463 / % possible obs: 99 % / Redundancy: 9.3 % / Biso Wilson estimate: 46.27 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.062 / Rrim(I) all: 0.192 / Χ2: 0.853 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.3-4.375.90.6793800.8230.2770.7370.86895
4.37-4.456.40.6443860.8320.2590.6970.82396.3
4.45-4.546.40.6154080.9030.2420.6640.87198.3
4.54-4.6370.6114050.8580.2350.6580.94799.5
4.63-4.737.60.4944120.9490.180.5280.92398.6
4.73-4.848.50.5044030.9410.1750.5350.92599.5
4.84-4.968.60.4944230.9450.1740.5250.913100
4.96-5.19.50.4734000.9380.1570.50.911100
5.1-5.2510.20.5074320.9680.1640.5330.86599.3
5.25-5.42110.5044020.9660.1560.5290.793100
5.42-5.6111.30.4354260.9770.1340.4560.838100
5.61-5.8310.60.3854160.9710.1230.4050.83899.8
5.83-6.1120.3794410.9760.1140.3960.79799.5
6.1-6.4211.40.3174020.9780.0960.3310.78399.5
6.42-6.8212.40.2724400.9860.0790.2830.769100
6.82-7.3512.20.1874420.9920.0550.1950.811100
7.35-8.0811.60.1344300.9950.0410.140.865100
8.08-9.259.60.0984490.990.0330.1041.03299.6
9.25-11.636.90.0654500.9950.0260.070.9297.4
11.63-506.70.0545160.9940.0240.0590.69297.5

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Processing

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

4zpk


Resolution: 4.274→15.969 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3146 384 5.03 %
Rwork0.2489 7255 -
obs0.2523 7639 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.84 Å2 / Biso mean: 50.1771 Å2 / Biso min: 22.04 Å2
Refinement stepCycle: final / Resolution: 4.274→15.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 656 0 0 5436
Num. residues----633
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.274-4.87640.3045980.2655198078
4.8764-6.08670.3451530.28152557100
6.0867-15.9690.29271330.2129271899

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