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- PDB-44hp: Drosophila AHR PAS-B (M284C/Y336L)-ARNT PAS-B heterodimer bound t... -

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Basic information

Entry
Database: PDB / ID: 44hp
TitleDrosophila AHR PAS-B (M284C/Y336L)-ARNT PAS-B heterodimer bound to alpha-naphthoflavone
Components
  • Ahr homolog spineless
  • Aryl hydrocarbon receptor nuclear translocator
KeywordsTRANSCRIPTION / Drosophila AHR / Spineless / PAS-B domain / alpha-naphthoflavone / ARNT
Function / homology
Function and homology information


regulation of R7 cell differentiation / antennal development / specification of animal organ identity / imaginal disc-derived leg segmentation / antennal morphogenesis / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor ...regulation of R7 cell differentiation / antennal development / specification of animal organ identity / imaginal disc-derived leg segmentation / antennal morphogenesis / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / male courtship behavior / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / intestinal epithelial structure maintenance / embryonic placenta development / G1 to G0 transition / regulation of dendrite morphogenesis / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / cis-regulatory region sequence-specific DNA binding / intracellular receptor signaling pathway / xenobiotic metabolic process / positive regulation of glycolytic process / RNA polymerase II transcription regulator complex / memory / negative regulation of inflammatory response / response to toxic substance / nuclear receptor activity / sequence-specific double-stranded DNA binding / transcription regulator complex / cellular response to oxidative stress / sequence-specific DNA binding / response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / 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 ...Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / 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
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / Ahr homolog spineless / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDai, S.Y. / Tang, J.M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021RC2034 China
CitationJournal: To Be Published
Title: ARNT association reshapes ligand recognition by AHR PAS-B domain
Authors: Dai, S.Y. / Tang, J.M.
History
DepositionJul 29, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ahr homolog spineless
B: Aryl hydrocarbon receptor nuclear translocator
C: Ahr homolog spineless
D: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67711
Polymers52,7144
Non-polymers9647
Water25214
1
A: Ahr homolog spineless
B: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8876
Polymers26,3572
Non-polymers5304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-76 kcal/mol
Surface area10920 Å2
MethodPISA
2
C: Ahr homolog spineless
D: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7915
Polymers26,3572
Non-polymers4343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-66 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.641, 107.290, 62.268
Angle α, β, γ (deg.)90.00, 123.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ahr homolog spineless


Mass: 13733.611 Da / Num. of mol.: 2 / Fragment: PAS-B domain / Mutation: M284C/Y336L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ss, CG6993 / Production host: Escherichia coli (E. coli) / References: UniProt: O61543
#2: 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: 12623.298 Da / Num. of mol.: 2 / Fragment: PAS-B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Production host: Escherichia coli (E. coli) / References: UniProt: P53762

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Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE


Mass: 272.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium arsenate (pH 6.5), 0.2 M magnesium chloride, and 1.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.6→21.2 Å / Num. obs: 18136 / % possible obs: 99.2 % / Redundancy: 4.3 % / CC1/2: 0.98 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 1819 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
PDB_EXTRACTV1.0data extraction
HKL-3000V721data reduction
HKL-3000V721data scaling
PHASERV2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→21.2 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 837 -
Rwork0.23 --
obs-18136 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→21.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 59 14 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033552
X-RAY DIFFRACTIONf_angle_d0.5994807
X-RAY DIFFRACTIONf_dihedral_angle_d4.988497
X-RAY DIFFRACTIONf_chiral_restr0.04514
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.770.34821490.29492871X-RAY DIFFRACTION100
2.77-2.990.37361230.28512919X-RAY DIFFRACTION100
2.99-3.290.31321490.24312871X-RAY DIFFRACTION100
3.29-3.760.25121340.22212876X-RAY DIFFRACTION99
3.76-4.730.21841350.18212902X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63830.35620.45680.26270.32640.42530.1478-0.20850.04490.0214-0.37310.70950.3252-0.55030.00270.38380.02110.08470.5361-0.08830.598518.597810.87317.9764
20.1606-0.1704-0.32790.13360.18660.2438-0.6928-0.21850.70490.00220.63390.2695-0.5234-0.8992-0.0020.67170.11580.040.57610.02960.520221.4916.546717.0828
31.5371-0.2236-0.15751.33950.01581.2910.0783-0.0405-0.0507-0.22610.03360.08720.3271-0.1254-0.00010.4348-0.0223-0.04170.3092-0.01570.319928.63917.23516.9238
41.86781.2802-1.21661.69790.10020.94230.0328-0-0.3270.3354-0.02520.04840.0979-0.07490.00020.5051-0.0525-0.07350.3842-0.06110.402625.03142.40338.1612
51.82380.798-1.20741.11340.611.61780.2052-0.65270.0440.2386-0.12760.25030.0123-0.3288-00.4598-0.05940.04730.44610.00040.353543.820320.396316.2469
60.4728-0.1696-0.15811.41740.21860.39590.05150.03450.44070.1904-0.20670.2684-0.5932-0.0149-0.00020.4314-0.06980.09690.4891-0.03010.448749.699929.34027.1387
71.18620.6656-0.52321.0808-1.1130.73850.2753-0.1711-0.07240.278-0.38710.39870.9118-0.4020.00240.3824-0.06830.04640.44950.00670.449252.901823.23210.5334
80.48170.8963-0.56171.31040.08611.1019-0.12330.15630.4165-0.2253-0.0959-0.0703-0.02310.3156-0.00020.47620.0060.03370.3369-0.00640.410544.047718.77895.3194
90.5002-0.44310.04220.4099-0.37770.5438-0.195-0.5561-0.4757-0.5864-0.35540.7758-0.40470.0864-0.00060.50860.0289-0.03040.43330.06250.492435.093942.46788.0903
10-0.0385-0.01810.02510.1591-0.09280.0393-0.5731-0.6161-0.26660.004-0.15060.4353-0.00530.29750.00020.55480.0388-0.08690.67770.03080.350336.478140.499216.5052
110.1097-0.1368-0.37960.08890.43341.6540.3086-0.8043-0.8513-0.5472-0.1424-1.04992.2318-0.4127-0.00630.58450.02240.06480.54120.05350.535432.745433.088419.118
121.09050.40170.10340.26110.20781.6798-0.05480.2483-0.11980.00380.3240.24810.0931-0.627700.3860.06450.01080.27760.02110.397524.970843.11284.9682
130.77590.00390.35110.3270.30430.2760.3192-1.0274-0.04780.49540.47561.0347-0.3712-0.5550.03120.48610.1110.05660.58930.16030.361623.707243.558917.9419
140.0471-0.30680.06160.76030.16930.5274-0.04240.0625-0.31470.1235-0.2112-0.0935-0.5372-0.0622-0.0050.36740.03760.0120.45040.09880.389131.651747.29677.8465
150.8693-0.65670.40761.78831.47063.18810.3303-0.04860.9898-0.04911.6065-1.9517-0.50862.24020.39090.3898-0.02930.07910.34260.01620.325737.162145.09074.521
160.34710.2186-0.01340.25560.2420.2671-0.4826-1.25250.37730.96120.13360.9032-0.9687-0.3928-0.00650.61210.11350.07030.7032-0.02390.574320.947455.737515.6286
174.0081.24670.45051.17330.94761.3880.3053-0.7321-1.1922-0.1886-0.3464-0.0079-0.4259-0.0557-0.00040.4707-0.0214-0.09760.73190.23980.87677.913128.817210.815
181.6955-1.2508-0.33933.44410.65190.13860.3069-1.825-0.3178-0.3301-1.0769-0.1344-0.38950.3127-0.7211-0.0805-0.1150.11541.22320.21330.7352-1.343529.012713.5715
190.79080.42230.94840.90610.30921.4912-0.4530.6289-0.6136-0.40330.09390.08210.3841-0.8178-0.00440.44020.0743-0.09290.37840.04760.599210.598134.09015.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 285 )
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 354 )
4X-RAY DIFFRACTION4chain 'A' and (resid 355 through 381 )
5X-RAY DIFFRACTION5chain 'B' and (resid 362 through 391 )
6X-RAY DIFFRACTION6chain 'B' and (resid 392 through 417 )
7X-RAY DIFFRACTION7chain 'B' and (resid 418 through 435 )
8X-RAY DIFFRACTION8chain 'B' and (resid 436 through 464 )
9X-RAY DIFFRACTION9chain 'C' and (resid 269 through 280 )
10X-RAY DIFFRACTION10chain 'C' and (resid 281 through 292 )
11X-RAY DIFFRACTION11chain 'C' and (resid 293 through 299 )
12X-RAY DIFFRACTION12chain 'C' and (resid 300 through 331 )
13X-RAY DIFFRACTION13chain 'C' and (resid 332 through 342 )
14X-RAY DIFFRACTION14chain 'C' and (resid 343 through 355 )
15X-RAY DIFFRACTION15chain 'C' and (resid 356 through 368 )
16X-RAY DIFFRACTION16chain 'C' and (resid 369 through 381 )
17X-RAY DIFFRACTION17chain 'D' and (resid 362 through 422 )
18X-RAY DIFFRACTION18chain 'D' and (resid 423 through 435 )
19X-RAY DIFFRACTION19chain 'D' and (resid 436 through 464 )

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