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- PDB-7vna: drosophlia AHR PAS-B domain -

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Basic information

Entry
Database: PDB / ID: 7vna
Titledrosophlia AHR PAS-B domain
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 / rhythmic process / transcription cis-regulatory region binding / protein heterodimerization activity / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Ahr homolog spineless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.597 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 10, 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

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Assembly

Deposited unit
A: Ahr homolog spineless


Theoretical massNumber of molelcules
Total (without water)13,8121
Polymers13,8121
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.259, 46.787, 81.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Ahr homolog spineless


Mass: 13811.681 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.47 %
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 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.58 Å / Relative weight: 1
ReflectionResolution: 2.59→31.6 Å / Num. obs: 4172 / % possible obs: 95.1 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 17.7
Reflection shellResolution: 2.6→2.65 Å / Rmerge(I) obs: 0.578 / Num. unique obs: 133

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Processing

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

3f1o


Resolution: 2.597→31.596 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 219 5.25 %
Rwork0.2104 3953 -
obs0.2125 4172 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.55 Å2 / Biso mean: 38.2332 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.597→31.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 0 11 915
Biso mean---31.9 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002921
X-RAY DIFFRACTIONf_angle_d0.5011240
X-RAY DIFFRACTIONf_chiral_restr0.035130
X-RAY DIFFRACTIONf_plane_restr0.002158
X-RAY DIFFRACTIONf_dihedral_angle_d12.095541
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-3.27130.34481130.2374180290
3.2713-31.5960.20951060.22151100
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)
11.83740.49810.70591.82120.39581.6504-0.11580.36320.2442-0.09540.38090.54560.1517-0.2271-0.12340.4183-0.037-0.00810.36030.14640.3313.0195-11.1562-15.8655
23.0205-2.52351.18054.3085-0.51292.713-0.0397-0.1145-0.58060.7180.1356-0.47870.06340.50510.07620.4734-0.0101-0.0550.33270.06010.38326.149-20.0668-19.4738
32.98811.8065-0.01153.78791.73862.92370.12790.13020.11830.06-0.1652-0.01280.0287-0.2541-0.08940.30570.0050.02130.29040.07460.24136.2339-1.5585-24.0093
44.3658-1.4067-0.46096.9659-0.7011.48370.00430.16270.23350.023-0.287-0.44210.1403-0.45060.18370.2993-0.0107-0.01310.4457-0.07650.44243.1907-12.8716-29.9773
51.127-0.43370.88510.3876-0.13770.9506-0.2568-1.41870.81740.8331-0.12810.23440.4255-0.3791-0.12170.42220.0010.09980.77710.02730.3847-0.357-2.186-10.891
62.405-0.32840.05812.61110.41980.4670.22130.3607-0.1869-0.3079-0.11010.080.3477-0.21960.1450.25270.00160.00170.43740.02230.3011-2.4756-7.0412-26.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 268 through 284 )A268 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 301 )A285 - 301
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 330 )A302 - 330
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 346 )A331 - 346
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 357 )A347 - 357
6X-RAY DIFFRACTION6chain 'A' and (resid 358 through 381 )A358 - 381

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