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- PDB-5v0l: Crystal structure of the AHR-ARNT heterodimer in complex with the DRE -

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Basic information

Entry
Database: PDB / ID: 5v0l
TitleCrystal structure of the AHR-ARNT heterodimer in complex with the DRE
Components
  • (Aryl hydrocarbon ...) x 2
  • DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / AHR / ARNT / transcription factor / heterodimer / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / reactive oxygen species biosynthetic process / Phase I - Functionalization of compounds ...circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / reactive oxygen species biosynthetic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / kidney morphogenesis / omega-hydroxylase P450 pathway / arachidonic acid omega-hydroxylase activity / positive regulation of growth rate / lymphocyte homeostasis / regulation of adaptive immune response / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / cardiac left ventricle morphogenesis / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / negative regulation of osteoblast proliferation / cellular response to toxic substance / reproductive structure development / prostate gland development / aryl hydrocarbon receptor complex / B-1 B cell homeostasis / positive regulation of protein sumoylation / post-embryonic hemopoiesis / Xenobiotics / negative regulation of DNA biosynthetic process / camera-type eye development / vasculature development / negative regulation of systemic arterial blood pressure / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / blood circulation / blood vessel morphogenesis / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of vasoconstriction / branching involved in blood vessel morphogenesis / immune system process / blood vessel development / E-box binding / T cell homeostasis / aryl hydrocarbon receptor binding / B cell homeostasis / protein localization to nucleus / positive regulation of cell size / toxic substance binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / negative regulation of osteoblast differentiation / blood vessel remodeling / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / ovarian follicle development / spleen development / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / xenobiotic metabolic process / positive regulation of glycolytic process / B cell differentiation / positive regulation of erythrocyte differentiation / liver development / Hsp90 protein binding / circadian regulation of gene expression / cell morphogenesis / response to organic cyclic compound / PPARA activates gene expression / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / protein-folding chaperone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / nuclear body / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription
Similarity search - Function
Aryl hydrocarbon receptor / 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 DNA-binding domain superfamily ...Aryl hydrocarbon receptor / 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 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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Aryl hydrocarbon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSeok, S.-H. / Lee, W. / Jiang, L. / Bradfield, C.A. / Xing, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM096060-01 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex.
Authors: Seok, S.H. / Lee, W. / Jiang, L. / Molugu, K. / Zheng, A. / Li, Y. / Park, S. / Bradfield, C.A. / Xing, Y.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Aryl hydrocarbon receptor
C: DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')
D: DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3248
Polymers67,7274
Non-polymers5964
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-52 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.199, 64.364, 157.725
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Aryl hydrocarbon ... , 2 types, 2 molecules AB

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 31028.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Plasmid: pQLinkH
Details (production host): Vectors for co-expression of proteins
Production host: Escherichia coli (E. coli) / References: UniProt: P27540
#2: Protein Aryl hydrocarbon receptor / / AhR


Mass: 27151.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ahr / Plasmid: pQLinkH
Details (production host): Vectors for co-expression of proteins
Production host: Escherichia coli (E. coli) / References: UniProt: P30561

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')


Mass: 5307.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')


Mass: 4239.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 10%-12% PEG 20000, 4-6% Tacsimate pH 7.0 or 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 6690 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rpim(I) all: 0.075 / Net I/σ(I): 11
Reflection shellResolution: 3.9→3.97 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 669 / Rpim(I) all: 0.592 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 4→39.685 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3226 332 4.98 %
Rwork0.2852 --
obs0.2872 6660 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→39.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 640 40 0 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023594
X-RAY DIFFRACTIONf_angle_d0.6714971
X-RAY DIFFRACTIONf_dihedral_angle_d15.5072051
X-RAY DIFFRACTIONf_chiral_restr0.087559
X-RAY DIFFRACTIONf_plane_restr0.003527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-5.03810.4331640.35313143X-RAY DIFFRACTION100
5.0381-39.68670.29411680.26573185X-RAY DIFFRACTION99

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