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- PDB-7vni: AHR-ARNT PAS-B heterodimer -

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Basic information

Entry
Database: PDB / ID: 7vni
TitleAHR-ARNT PAS-B heterodimer
Components
  • Ahr homolog spineless
  • Aryl hydrocarbon receptor nuclear translocator
KeywordsTRANSCRIPTION / transcription factor / ligand binding domain
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 / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / 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 / 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 / male courtship behavior / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / regulation of dendrite morphogenesis / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / xenobiotic metabolic process / positive regulation of glycolytic process / response to toxic substance / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / memory / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / cell differentiation / response to hypoxia / transcription cis-regulatory region binding / 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 / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / 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
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: 1.997 Å
AuthorsDai, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2022
Title: Structural insight into the ligand binding mechanism of aryl hydrocarbon receptor.
Authors: Dai, S. / Qu, L. / Li, J. / Zhang, Y. / Jiang, L. / Wei, H. / Guo, M. / Chen, X. / Chen, Y.
History
DepositionOct 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,1077
Polymers53,8194
Non-polymers2883
Water7,584421
1
B: Ahr homolog spineless
D: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1024
Polymers26,9102
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-38 kcal/mol
Surface area11160 Å2
MethodPISA
2
A: Ahr homolog spineless
C: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0063
Polymers26,9102
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-18 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.030, 55.553, 77.095
Angle α, β, γ (deg.)90.000, 103.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ahr homolog spineless


Mass: 13811.681 Da / Num. of mol.: 2
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: 13097.854 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium arsenate (pH 6.5), 0.2 M MgCl2, 2 M (NH4)2SO4

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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 PILATUS 6M / Detector: PIXEL / Date: May 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.99→45 Å / Num. obs: 36452 / % possible obs: 96.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 1927 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1O

3f1o


Resolution: 1.997→44.908 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1999 5.48 %
Rwork0.1795 34450 -
obs0.1816 36449 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.76 Å2 / Biso mean: 31.8741 Å2 / Biso min: 10.87 Å2
Refinement stepCycle: final / Resolution: 1.997→44.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 15 421 3986
Biso mean--42.52 39.37 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063648
X-RAY DIFFRACTIONf_angle_d0.8254917
X-RAY DIFFRACTIONf_chiral_restr0.061519
X-RAY DIFFRACTIONf_plane_restr0.005626
X-RAY DIFFRACTIONf_dihedral_angle_d4.8492364
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9972-2.04720.28931180.2413204079
2.0472-2.10250.24951310.2061224687
2.1025-2.16440.25451450.202251097
2.1644-2.23430.22081440.1913246597
2.2343-2.31410.20471460.1752251497
2.3141-2.40670.19611440.1805248197
2.4067-2.51630.2071400.1847241093
2.5163-2.64890.22661460.1821252698
2.6489-2.81490.25331460.1879251798
2.8149-3.03220.2511470.1806252998
3.0322-3.33720.22481440.1726248595
3.3372-3.81990.21331490.1604256999
3.8199-4.81180.18131480.1502254397
4.8118-44.90.21351510.2039261597
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)
14.2019-0.2148-1.16744.23191.05683.5769-0.03830.76520.3069-0.01070.16520.4526-0.3845-0.4674-0.26680.20610.04860.02690.41950.11920.2189-20.143214.84571.2783
23.1454-2.1670.35686.7176-1.1212.80620.02530.44280.24870.29520.15990.1819-0.4314-0.088-0.23430.23670.01640.05260.47530.03430.2106-11.98469.8107-0.6327
32.2160.74941.30252.4873-0.97481.6640.19280.65160.7231-0.27450.15570.405-0.7396-0.1894-0.23910.78920.16840.3090.43030.22070.4519-16.657523.52340.2365
42.12621.0644-2.462.1124-0.70684.08990.05850.6290.00640.37760.07350.2431-0.0983-0.0178-0.54111.0259-0.1050.19410.6033-0.03220.49-7.952720.5004-0.9754
52.5329-2.411-3.16122.29842.97014.139-0.04941.03120.5584-1.33360.2292-0.4827-0.5491-0.3092-0.0450.3985-0.18480.00240.67940.19570.264-5.19213.922-0.103
62.5416-0.24490.181.6040.78082.2055-0.0260.2030.1889-0.05670.0579-0.202-0.0707-0.1905-0.05280.1282-0.04070.01990.2456-0.00180.1847-13.26376.661412.3531
73.23153.6286-2.22574.3632-1.65414.1117-0.12250.52710.7372-0.41930.1678-0.3472-0.40610.271-0.13870.2484-0.04660.05820.31130.11310.5246-11.656420.452511.3102
82.2575-0.3903-0.62891.2126-0.45712.24940.05180.73970.2652-0.28690.0636-0.1033-0.0326-0.36010.0170.1441-0.05360.02480.39190.03620.2714-17.86812.5367.781
92.9725-0.5634-0.31974.02060.69113.7866-0.0640.8410.0088-0.42350.06550.15540.0024-0.2071-0.0310.1774-0.01650.02690.48350.02380.2289-19.26697.07331.0787
104.8805-0.24040.29725.0376-1.27955.3253-0.0657-0.42210.80860.4722-0.07410.1987-0.7176-0.4582-0.16350.21350.0080.06150.2969-0.07470.3837-21.083618.621720.3701
111.8832-0.1883-0.19782.85481.06191.9155-0.26670.17310.77350.0760.03990.1156-0.3542-0.00930.0340.18710.0037-0.05970.1156-0.02710.33764.544619.723318.1745
120.3112-0.1408-0.63441.0999-0.40551.7627-0.19730.37170.66810.0423-0.02310.0181-0.4130.51370.06160.1929-0.0961-0.08770.19630.08690.341714.376917.688917.0316
134.60312.53752.3444.84232.19354.6561-0.05950.401-0.353-0.11750.1309-0.37810.12190.6388-0.02360.1820.01950.02190.18810.00250.1915.40346.109919.5612
144.4068-1.86591.58995.00072.28862.70440.42410.3038-0.69940.28540.19610.53570.7116-0.28360.11580.2698-0.0544-0.0440.22690.04980.38753.0547-1.149618.3889
150.4031-0.97510.08372.8374-0.71730.5951-0.2777-0.08890.62020.4041-0.0805-0.1907-0.34930.3242-0.77520.3362-0.041-0.0930.1624-0.02950.350613.895618.291325.9781
163.45030.85721.78611.77080.7652.80280.06080.0025-0.19190.1184-0.0269-0.0802-0.0296-0.2863-0.04090.13590.00340.0250.123-0.01960.15043.34577.371418.0828
173.11520.24521.26713.08721.88937.2942-0.0628-0.04150.14960.07880.09850.004-0.1863-0.2649-0.04120.1193-0.0030.0240.1195-0.01540.17582.961411.18419.5346
183.21240.54581.13050.6745-0.03730.8452-0.08690.4394-0.1985-0.24550.0242-0.1410.13220.109-1.56510.1241-0.315-0.18760.5406-0.16360.1478-30.3569-10.2426.6458
194.52372.99620.24965.35240.87630.16490.2460.7032-0.1856-0.36130.23560.26610.1332-0.4591-0.27530.1389-0.0244-0.02330.41640.06440.2136-37.74161.087116.3147
200.2738-0.5660.18921.2213-0.59831.8881-0.08420.4291-0.4831-0.4670.28380.13440.3907-0.31890.0370.3039-0.14710.00230.4914-0.13180.3549-36.3073-13.836410.1232
217.3398-3.99310.45524.78760.59094.55-0.13181.1719-0.2073-0.15220.36490.24030.6656-0.3728-0.20210.2799-0.1375-0.02970.3773-0.04130.4025-41.4629-13.013816.3673
221.6913-0.13150.27591.8207-0.06211.30860.00920.33120.0323-0.06610.08360.01410.14870.0346-0.09860.1106-0.0239-0.00940.22660.00430.1347-28.7624-0.847520.0149
237.92625.5402-1.30045.9465-1.1740.8942-0.21890.0769-0.4741-0.1120.0574-0.01830.4971-0.38460.12910.2751-0.09710.00670.242-0.05620.2158-28.4978-13.707120.5174
242.6937-0.73620.44542.95590.14122.22070.0940.80120.0112-0.4301-0.04690.21710.0805-0.222-0.03490.1503-0.0808-0.02190.4030.02850.1566-30.9397-2.121510.1819
252.5546-0.1-0.07454.55541.673.36970.11330.4014-0.4333-0.1492-0.0567-0.85940.48080.7091-0.1460.22380.080.06050.2553-0.02090.3357-15.7576-11.304318.1388
260.55370.16350.0892.6775-0.30920.84060.17280.0178-0.31130.16940.207-0.00611.0635-0.09020.50930.6566-0.0573-0.0288-0.14220.03580.1813-33.1415-13.123737.7966
271.36110.9389-0.23271.5807-1.22981.30560.0141-0.30370.05290.3901-0.09410.47550.6923-0.6883-0.50920.4824-0.07210.11490.2361-0.01870.2051-37.2866-2.671747.9275
282.8932-2.2407-1.88635.7852-1.15462.9202-0.24380.14160.467-0.25570.0982-0.4587-0.5135-0.30560.14380.4828-0.0272-0.07630.130.00630.2201-31.30117.772236.6456
290.46940.3167-0.11422.4878-0.45480.08960.0846-0.24-0.28450.5106-0.0985-0.3150.7625-0.2518-0.05730.8502-0.0414-0.06790.19080.03340.3107-30.4192-11.266849.6276
301.45110.5124-0.45161.8096-0.83122.7169-0.05710.04650.02460.41990.1146-0.1220.09030.03160.02570.24970.034-0.02380.0958-0.02450.1718-30.9958-2.17136.9222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 269 through 274 )B269 - 274
2X-RAY DIFFRACTION2chain 'B' and (resid 275 through 284 )B275 - 284
3X-RAY DIFFRACTION3chain 'B' and (resid 285 through 291 )B285 - 291
4X-RAY DIFFRACTION4chain 'B' and (resid 292 through 299 )B292 - 299
5X-RAY DIFFRACTION5chain 'B' and (resid 300 through 304 )B300 - 304
6X-RAY DIFFRACTION6chain 'B' and (resid 305 through 330 )B305 - 330
7X-RAY DIFFRACTION7chain 'B' and (resid 331 through 341 )B331 - 341
8X-RAY DIFFRACTION8chain 'B' and (resid 342 through 354 )B342 - 354
9X-RAY DIFFRACTION9chain 'B' and (resid 355 through 368 )B355 - 368
10X-RAY DIFFRACTION10chain 'B' and (resid 369 through 380 )B369 - 380
11X-RAY DIFFRACTION11chain 'D' and (resid 361 through 391 )D361 - 391
12X-RAY DIFFRACTION12chain 'D' and (resid 392 through 401 )D392 - 401
13X-RAY DIFFRACTION13chain 'D' and (resid 402 through 417 )D402 - 417
14X-RAY DIFFRACTION14chain 'D' and (resid 418 through 422 )D418 - 422
15X-RAY DIFFRACTION15chain 'D' and (resid 423 through 435 )D423 - 435
16X-RAY DIFFRACTION16chain 'D' and (resid 436 through 453 )D436 - 453
17X-RAY DIFFRACTION17chain 'D' and (resid 454 through 464 )D454 - 464
18X-RAY DIFFRACTION18chain 'A' and (resid 267 through 274 )A267 - 274
19X-RAY DIFFRACTION19chain 'A' and (resid 275 through 279 )A275 - 279
20X-RAY DIFFRACTION20chain 'A' and (resid 280 through 291 )A280 - 291
21X-RAY DIFFRACTION21chain 'A' and (resid 292 through 299 )A292 - 299
22X-RAY DIFFRACTION22chain 'A' and (resid 300 through 330 )A300 - 330
23X-RAY DIFFRACTION23chain 'A' and (resid 331 through 341 )A331 - 341
24X-RAY DIFFRACTION24chain 'A' and (resid 342 through 368 )A342 - 368
25X-RAY DIFFRACTION25chain 'A' and (resid 369 through 381 )A369 - 381
26X-RAY DIFFRACTION26chain 'C' and (resid 362 through 395 )C362 - 395
27X-RAY DIFFRACTION27chain 'C' and (resid 396 through 417 )C396 - 417
28X-RAY DIFFRACTION28chain 'C' and (resid 418 through 422 )C418 - 422
29X-RAY DIFFRACTION29chain 'C' and (resid 423 through 435 )C423 - 435
30X-RAY DIFFRACTION30chain 'C' and (resid 436 through 464 )C436 - 464

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