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

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Basic information

Entry
Database: PDB / ID: 8xsa
TitleCrystal structure of the DNA-bound AHR-ARNT heterodimer in complex with Indigo
Components
  • (Aryl hydrocarbon ...) x 2
  • DNAF
  • DNAR
KeywordsTRANSCRIPTION / Aryl hydrocarbon receptor / HLH-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 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / Aryl hydrocarbon receptor signalling / cellular response to molecule of bacterial origin ...Phase I - Functionalization of compounds / Endogenous sterols / Xenobiotics / Aryl hydrocarbon receptor signalling / regulation of B cell proliferation / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / Aryl hydrocarbon receptor signalling / cellular response to molecule of bacterial origin / 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 / aryl hydrocarbon receptor binding / TFIID-class transcription factor complex binding / positive regulation of vascular endothelial growth factor production / Endogenous sterols / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / NPAS4 regulates expression of target genes / positive regulation of endothelial cell proliferation / xenobiotic metabolic process / cellular response to forskolin / TBP-class protein binding / positive regulation of erythrocyte differentiation / cellular response to cAMP / positive regulation of glycolytic process / Hsp90 protein binding / PPARA activates gene expression / response to toxic substance / negative regulation of inflammatory response / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / rhythmic process / cellular response to oxidative stress / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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: 2.597 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)101,7796
Polymers101,3624
Non-polymers4172
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-101 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.016, 98.837, 80.307
Angle α, β, γ (deg.)90.00, 90.41, 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, 146 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-A1LWK / 2-(3-oxidanyl-1H-indol-2-yl)indol-3-one


Mass: 262.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 55.08 %
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: BL19U1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.597→50 Å / Num. obs: 32695 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.094 / Χ2: 0.991 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.644.80.58115680.780.9360.2850.6511.07597.1
2.64-2.694.70.52716210.8130.9470.2630.5921.12898.7
2.69-2.7450.49216150.8360.9540.240.551.12799.5
2.74-2.85.20.42516140.8840.9690.2030.4731.11699.8
2.8-2.865.20.37516640.9080.9760.1810.4181.10299.8
2.86-2.935.10.32416220.9340.9830.1590.3621.04399.8
2.93-35.10.27816570.9460.9860.1360.311.02599.7
3-3.085.30.23916340.960.990.1140.2661.04599.6
3.08-3.175.30.18316120.9840.9960.0870.2031.10399.8
3.17-3.2850.12716300.9950.9990.0630.1421.0999.8
3.28-3.395.20.12416250.9890.9970.0590.1371.06299.9
3.39-3.535.20.09616560.9950.9990.0460.1071.00799.8
3.53-3.6950.08316150.9940.9980.0410.0930.975100
3.69-3.885.30.07316450.9950.9990.0350.0810.91799.9
3.88-4.135.20.06216440.9950.9990.030.0690.90799.9
4.13-4.455.10.05216500.9960.9990.0250.0580.89199.9
4.45-4.895.20.04816330.9960.9990.0230.0540.80799.7
4.89-5.65.30.04816620.9960.9990.0230.0540.74799.6
5.6-7.055.10.05116600.9950.9990.0240.0560.75599.9
7.05-5050.04416680.9960.9990.0220.0490.95598.3

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.597→30.48 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 2008 6.49 %
Rwork0.1949 --
obs0.1984 30934 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.597→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 855 28 144 6066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046141
X-RAY DIFFRACTIONf_angle_d0.6158462
X-RAY DIFFRACTIONf_dihedral_angle_d11.7994122
X-RAY DIFFRACTIONf_chiral_restr0.041935
X-RAY DIFFRACTIONf_plane_restr0.005934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.597-2.66190.31961070.25361479X-RAY DIFFRACTION68
2.6619-2.73380.29491170.26521684X-RAY DIFFRACTION77
2.7338-2.81420.35481260.25721848X-RAY DIFFRACTION85
2.8142-2.9050.33791410.26132053X-RAY DIFFRACTION93
2.905-3.00870.32451520.25382118X-RAY DIFFRACTION98
3.0087-3.12910.31011540.23582170X-RAY DIFFRACTION100
3.1291-3.27130.27051460.2162189X-RAY DIFFRACTION99
3.2713-3.44360.29111530.22612196X-RAY DIFFRACTION100
3.4436-3.6590.2811560.18472196X-RAY DIFFRACTION100
3.659-3.9410.22241490.17182181X-RAY DIFFRACTION100
3.941-4.33650.21111490.15872191X-RAY DIFFRACTION100
4.3365-4.96170.19491560.14612214X-RAY DIFFRACTION100
4.9617-6.24240.20931540.18352216X-RAY DIFFRACTION100
6.2424-30.480.21241480.18352191X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 19.1306 Å / Origin y: 2.7815 Å / Origin z: 12.7349 Å
111213212223313233
T0.3537 Å20.0694 Å20.0232 Å2-0.204 Å20.0365 Å2--0.2242 Å2
L1.1141 °20.227 °2-0.0769 °2-0.4324 °20.1127 °2--0.219 °2
S-0.0018 Å °-0.2066 Å °-0.0314 Å °0.0269 Å °-0.0076 Å °-0.0323 Å °0.0218 Å °0.0721 Å °-0.0064 Å °
Refinement TLS groupSelection details: all

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