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- PDB-5y7y: Crystal structure of AhRR/ARNT complex -

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Basic information

Entry
Database: PDB / ID: 5y7y
TitleCrystal structure of AhRR/ARNT complex
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Aryl hydrocarbon receptor repressor
KeywordsTRANSCRIPTION / transcriptional regulation
Function / homology
Function and homology information


nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / intracellular receptor signaling pathway / Xenobiotics / Phase I - Functionalization of compounds / Endogenous sterols / xenobiotic metabolic process / PPARA activates gene expression / nuclear receptor activity ...nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / intracellular receptor signaling pathway / Xenobiotics / Phase I - Functionalization of compounds / Endogenous sterols / xenobiotic metabolic process / PPARA activates gene expression / nuclear receptor activity / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription regulator complex / transcription cis-regulatory region binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Aryl hydrocarbon receptor repressor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / Nuclear translocator / 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 ...Aryl hydrocarbon receptor repressor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / Nuclear translocator / 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
Aryl hydrocarbon receptor repressor / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSakurai, S. / Shimizu, T. / Ohto, U.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The crystal structure of the AhRR-ARNT heterodimer reveals the structural basis of the repression of AhR-mediated transcription.
Authors: Sakurai, S. / Shimizu, T. / Ohto, U.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor repressor
B: Aryl hydrocarbon receptor nuclear translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3735
Polymers64,0962
Non-polymers2763
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-52 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.362, 78.362, 129.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Aryl hydrocarbon receptor repressor / AhRR / Class E basic helix-loop-helix protein 77 / bHLHe77


Mass: 28464.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHRR, BHLHE77, KIAA1234 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A9YTQ3
#2: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein


Mass: 35631.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 82-147,154-230,257-271,301-312 / Mutation: deletions 148-153,231-256,272-300,313-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARNT / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BE97
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30559 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 28.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.653 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.237 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26832 1542 5 %RANDOM
Rwork0.23352 ---
obs0.23527 29016 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.827 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å2-0 Å2
2--2.27 Å2-0 Å2
3----4.54 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 18 22 3782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193830
X-RAY DIFFRACTIONr_bond_other_d0.0040.023701
X-RAY DIFFRACTIONr_angle_refined_deg0.9671.9625161
X-RAY DIFFRACTIONr_angle_other_deg0.71638487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75322.967182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60215680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6391535
X-RAY DIFFRACTIONr_chiral_restr0.0530.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0927.9211847
X-RAY DIFFRACTIONr_mcbond_other2.0867.921846
X-RAY DIFFRACTIONr_mcangle_it3.78411.8372293
X-RAY DIFFRACTIONr_mcangle_other3.78411.8372294
X-RAY DIFFRACTIONr_scbond_it1.6358.0241983
X-RAY DIFFRACTIONr_scbond_other1.6358.0241983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.96611.9862869
X-RAY DIFFRACTIONr_long_range_B_refined5.90861.3924160
X-RAY DIFFRACTIONr_long_range_B_other5.90861.3954161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 117 -
Rwork0.294 2095 -
obs--99.02 %

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