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- PDB-8xs7: Crystal structure of the DNA-bound AHR-ARNT heterodimer in comple... -

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Basic information

Entry
Database: PDB / ID: 8xs7
TitleCrystal structure of the DNA-bound AHR-ARNT heterodimer in complex with FICZ
Components
  • (Aryl hydrocarbon ...) x 2
  • DNAF
  • DNAR
KeywordsTRANSCRIPTION / Aryl hydrocarbon receptor / FICZ / bHLH-PAS
Function / homology
Function and homology information


Phase I - Functionalization of compounds / Endogenous sterols / Xenobiotics / Aryl hydrocarbon receptor signalling / regulation of B cell proliferation / cellular response to molecule of bacterial origin / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process ...Phase I - Functionalization of compounds / Endogenous sterols / Xenobiotics / Aryl hydrocarbon receptor signalling / regulation of B cell proliferation / cellular response to molecule of bacterial origin / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / negative regulation of T cell mediated immune response to tumor cell / positive regulation of protein sumoylation / Xenobiotics / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / TFIID-class transcription factor complex binding / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / cellular response to cAMP / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / TBP-class protein binding / cellular response to forskolin / xenobiotic metabolic process / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / Hsp90 protein binding / transcription coactivator binding / PPARA activates gene expression / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / response to toxic substance / nuclear receptor activity / sequence-specific double-stranded DNA binding / rhythmic process / cellular response to oxidative stress / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear body / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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 ...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 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
: / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / DNA / DNA (> 10) / Aryl hydrocarbon receptor / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDiao, X. / Shang, Q. / Wu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82373876 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex.
Authors: Diao, X. / Shang, Q. / Guo, M. / Huang, Y. / Zhang, M. / Chen, X. / Liang, Y. / Sun, X. / Zhou, F. / Zhuang, J. / Liu, S.J. / Vogel, C.F.A. / Rastinejad, F. / Wu, D.
History
DepositionJan 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: 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

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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: DNAF
D: DNAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8016
Polymers101,3624
Non-polymers4392
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-102 kcal/mol
Surface area36190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.330, 98.514, 80.372
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 43231.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27540
#2: Protein Aryl hydrocarbon receptor


Mass: 45242.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: AHR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I3LF82

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNAF


Mass: 6473.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNAR


Mass: 6415.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 52 molecules

#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-A1LWI / 5,11-dihydroindolo[3,2-b]carbazole-12-carbaldehyde


Mass: 284.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: potassium citrate tribasic monohydrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.77→34.18 Å / Num. obs: 27183 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID
2.77-2.846.80.7332.219951
12.39-34.180.03227.23171

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→34.164 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 1992 7.35 %
Rwork0.2065 --
obs0.2108 27113 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→34.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 855 30 50 5934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036137
X-RAY DIFFRACTIONf_angle_d0.6178462
X-RAY DIFFRACTIONf_dihedral_angle_d12.0844118
X-RAY DIFFRACTIONf_chiral_restr0.04936
X-RAY DIFFRACTIONf_plane_restr0.005934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.83860.36351390.31821757X-RAY DIFFRACTION98
2.8386-2.91530.36521380.31121783X-RAY DIFFRACTION100
2.9153-3.00110.37351440.27711806X-RAY DIFFRACTION100
3.0011-3.09790.33581450.26391786X-RAY DIFFRACTION100
3.0979-3.20850.26551410.23241780X-RAY DIFFRACTION100
3.2085-3.33690.24441430.22991770X-RAY DIFFRACTION99
3.3369-3.48860.29991380.2261788X-RAY DIFFRACTION100
3.4886-3.67230.29461450.19791785X-RAY DIFFRACTION100
3.6723-3.90210.2871450.19671799X-RAY DIFFRACTION100
3.9021-4.20290.2711440.17761791X-RAY DIFFRACTION100
4.2029-4.62490.21291440.15511810X-RAY DIFFRACTION100
4.6249-5.29210.21081450.16111811X-RAY DIFFRACTION100
5.2921-6.65930.21811420.20931818X-RAY DIFFRACTION100
6.6593-34.1640.25891390.19711837X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.1339 Å / Origin y: 2.8818 Å / Origin z: 13.0553 Å
111213212223313233
T0.3101 Å20.0501 Å20.0587 Å2-0.2319 Å20.0576 Å2--0.3503 Å2
L1.3892 °20.1478 °2-0.0897 °2-0.4909 °20.1261 °2--0.3303 °2
S0.0187 Å °-0.3059 Å °-0.0486 Å °-0.0038 Å °-0.0162 Å °-0.0475 Å °-0.0002 Å °0.0876 Å °-0.0018 Å °
Refinement TLS groupSelection details: all

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