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- PDB-7vnh: drosophlia AHR PAS-B domain bound by the antagonist alpha-naphtho... -

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Basic information

Entry
Database: PDB / ID: 7vnh
Titledrosophlia AHR PAS-B domain bound by the antagonist alpha-naphthoflavone
ComponentsAhr homolog spineless
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 / male courtship behavior / aryl hydrocarbon receptor complex / regulation of dendrite morphogenesis / xenobiotic metabolic process / memory ...regulation of R7 cell differentiation / antennal development / specification of animal organ identity / imaginal disc-derived leg segmentation / antennal morphogenesis / male courtship behavior / aryl hydrocarbon receptor complex / regulation of dendrite morphogenesis / xenobiotic metabolic process / memory / nuclear receptor activity / transcription cis-regulatory region binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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 ...Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.402 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ahr homolog spineless
B: Ahr homolog spineless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers27,6232
Non-polymers5452
Water82946
1
A: Ahr homolog spineless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0842
Polymers13,8121
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ahr homolog spineless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0842
Polymers13,8121
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.235, 60.235, 121.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 269 through 288 or (resid 289...
21(chain B and (resid 269 through 284 or (resid 285...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLY(chain A and (resid 269 through 288 or (resid 289...AA269 - 2888 - 27
12LYSLYSLYSLYS(chain A and (resid 269 through 288 or (resid 289...AA28928
13ASNASNARGARG(chain A and (resid 269 through 288 or (resid 289...AA269 - 3818 - 120
14ASNASNARGARG(chain A and (resid 269 through 288 or (resid 289...AA269 - 3818 - 120
15ASNASNARGARG(chain A and (resid 269 through 288 or (resid 289...AA269 - 3818 - 120
16ASNASNARGARG(chain A and (resid 269 through 288 or (resid 289...AA269 - 3818 - 120
21ASNASNMETMET(chain B and (resid 269 through 284 or (resid 285...BB269 - 2848 - 23
22ASPASPASPASP(chain B and (resid 269 through 284 or (resid 285...BB28524

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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: 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: isolated from a natural source / Formula: C19H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 7.0, 0.2 M NaCl, 0.8 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.58 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.58 Å / Relative weight: 1
ReflectionResolution: 2.4→30.3 Å / Num. obs: 9195 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.992 / Net I/σ(I): 16.3
Reflection shellResolution: 2.4→2.45 Å / Num. unique obs: 526 / CC1/2: 0.77

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Processing

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

3f1o


Resolution: 2.402→30.262 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 920 10.01 %
Rwork0.231 8274 -
obs0.2347 9194 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.36 Å2 / Biso mean: 43.8797 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 2.402→30.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 42 46 1886
Biso mean--41.46 37.23 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041892
X-RAY DIFFRACTIONf_angle_d0.72545
X-RAY DIFFRACTIONf_chiral_restr0.048260
X-RAY DIFFRACTIONf_plane_restr0.002318
X-RAY DIFFRACTIONf_dihedral_angle_d5.4461097
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A850X-RAY DIFFRACTION6.038TORSIONAL
12B850X-RAY DIFFRACTION6.038TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.402-2.52820.35261240.3148111797
2.5282-2.68650.36931290.29731156100
2.6865-2.89370.35361290.29861162100
2.8937-3.18470.34081300.25551175100
3.1847-3.64480.23991310.22011177100
3.6448-4.58950.21771340.18251199100
4.5895-30.260.22871430.2159128899
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)
11.8651-1.31840.46981.3973-1.37763.19180.0543-0.27370.09860.0560.0567-0.15780.09560.7491-0.19640.3099-0.0279-0.04670.372-0.00610.3456-16.82211.973413.1751
23.25150.2822-1.06562.04133.30563.24370.2851-1.0242-0.7241-0.5512-0.7859-1.5096-0.2794-1.1434-0.03230.69230.0201-0.25120.69960.21080.5121-9.83335.298119.1732
31.5317-1.7619-0.3623.7307-1.31852.9076-0.01020.08320.07830.0538-0.2024-0.2382-0.03650.54990.17090.3012-0.03920.01110.37550.02950.2686-21.55285.20127.5374
41.1267-0.5675-0.03422.0321-0.09121.46920.00760.1708-0.07770.4548-0.3729-0.04640.40890.25020.21580.39040.06520.00250.42120.02870.3381-19.7575.336613.2538
52.7117-0.85670.29122.7955-0.33451.0058-0.0627-0.4047-0.10130.3822-0.1269-0.23570.06920.0480.03830.33450.03950.03970.368-0.01360.2369-24.42664.832415.5093
63.4449-0.65112.91945.262-2.46295.31360.77330.8857-0.2899-1.16010.51480.9504-0.4713-0.2953-0.8210.53490.07660.02330.48670.07470.339-21.074613.4764-16.6241
78.82323.102-0.25437.32610.45947.65770.47810.22330.80980.36890.2714-0.0649-0.3670.2035-0.59550.310.01010.07660.3352-0.02150.3432-18.43389.6646-3.4457
82.6478-1.74940.12476.0977-0.59851.00160.19990.44380.8258-1.18280.1782-0.279-0.1655-0.7447-0.07730.4838-0.00740.04390.51270.11290.4847-16.318118.5748-16.3388
97.6958-0.6168-1.93194.1731.18193.74460.68330.661.02160.35480.6338-0.8581.37410.2008-0.6920.62680.0618-0.04320.7275-0.06741.0078-11.61423.3548-10.3012
105.9043-1.25220.27442.4654-1.09631.4867-0.5797-0.83230.47590.11430.5441-0.4132-0.13051.16550.02790.4598-0.0752-0.0110.5663-0.05530.4991-17.59419.145-3.628
111.7815-0.23240.34892.20661.04890.7778-0.0718-0.05440.1759-0.38640.15380.7-0.114-0.05410.07430.31280.0046-0.00350.3014-0.01730.3524-30.641710.5583-3.7912
123.71291.5932-0.58912.1644-0.02521.45090.03230.70430.5738-0.54520.0947-0.1996-0.10790.0371-0.22530.41020.03490.04530.31260.03090.4917-25.004124.3725-8.7731
131.4386-1.1274-0.75394.02960.69191.24220.08790.098-0.0103-0.0636-0.0832-0.27230.13740.0081-0.12520.3304-0.0322-0.00430.3482-0.06720.2568-23.65499.8549-11.005
144.88992.374-0.68625.7821-0.55162.5961-0.0593-0.0528-0.1083-0.8475-0.15860.3620.68770.02030.15160.39970.0021-0.08210.26820.00470.284-38.590322.8955-12.3446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 284 )A269 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 291 )A285 - 291
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 336 )A292 - 336
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 354 )A337 - 354
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 380 )A355 - 380
6X-RAY DIFFRACTION6chain 'B' and (resid 269 through 274 )B269 - 274
7X-RAY DIFFRACTION7chain 'B' and (resid 275 through 279 )B275 - 279
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 291 )B280 - 291
9X-RAY DIFFRACTION9chain 'B' and (resid 292 through 298 )B292 - 298
10X-RAY DIFFRACTION10chain 'B' and (resid 299 through 308 )B299 - 308
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 330 )B309 - 330
12X-RAY DIFFRACTION12chain 'B' and (resid 331 through 341 )B331 - 341
13X-RAY DIFFRACTION13chain 'B' and (resid 342 through 368 )B342 - 368
14X-RAY DIFFRACTION14chain 'B' and (resid 369 through 380 )B369 - 380

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