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- PDB-8g4a: Human ARNT PAS-B complexed with KG-548 small molecule -

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Basic information

Entry
Database: PDB / ID: 8g4a
TitleHuman ARNT PAS-B complexed with KG-548 small molecule
ComponentsAryl hydrocarbon receptor nuclear translocator
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / 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 ...nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / 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 / positive regulation of vascular endothelial growth factor production / embryonic placenta development / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / positive regulation of glycolytic process / positive regulation of erythrocyte differentiation / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / 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
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 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 ...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 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
: / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsXu, X. / Isiorho, E.A. / Pimentel Marcelino, L. / Gardner, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1818148 United States
CitationJournal: To Be Published
Title: Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids
Authors: Xu, X. / Gardner, K.H.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,1963
Polymers27,9132
Non-polymers2821
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, providing information on ligand homo dimer complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.135, 80.135, 100.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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 / HIF-1-beta / HIF1-beta


Mass: 13956.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27540
#2: Chemical ChemComp-YL8 / 5-[3,5-bis(trifluoromethyl)phenyl]-2H-tetrazole


Mass: 282.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H4F6N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.49 Å3/Da / Density % sol: 65 % / Description: diamond-like appearance
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 1.6 M magnesium sulfate, 2:1 (protein:condition)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.97→69.4 Å / Num. obs: 27007 / % possible obs: 99.76 % / Redundancy: 10 % / Biso Wilson estimate: 61.65 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.0166 / Rrim(I) all: 0.05186 / Net I/σ(I): 22.86
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 3.823 / Num. unique obs: 2701 / CC1/2: 0.354 / % possible all: 98.15

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
Blu-Icedata collection
autoPROCdata reduction
PHASERphasing
PDB-REDOrefinement
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→69.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.19 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22932 1979 7.3 %RANDOM
Rwork0.20404 ---
obs0.20583 25028 100 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å2-0 Å2
2---0.12 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.97→69.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 19 3 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0171828
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161592
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.8252474
X-RAY DIFFRACTIONr_angle_other_deg0.4351.563718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745.271221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3910318
X-RAY DIFFRACTIONr_chiral_restr0.060.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_mcbond_it4.8944.6842
X-RAY DIFFRACTIONr_mcbond_other4.8994.6842
X-RAY DIFFRACTIONr_mcangle_it6.1166.8711049
X-RAY DIFFRACTIONr_mcangle_other6.1146.8761050
X-RAY DIFFRACTIONr_scbond_it6.3665.261986
X-RAY DIFFRACTIONr_scbond_other6.3635.261987
X-RAY DIFFRACTIONr_scangle_other8.8647.6761426
X-RAY DIFFRACTIONr_long_range_B_refined10.5656.2281958
X-RAY DIFFRACTIONr_long_range_B_other10.55856.2211959
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 148 -
Rwork0.365 1833 -
obs--100 %
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)
17.55381.88110.48826.73640.47786.2460.3879-0.7281-0.22930.4571-0.2342-0.36380.1443-0.1125-0.15370.0657-0.0208-0.0420.15310.03410.0344-26.338-20.9521.798
23.5565-0.22610.98978.4706-1.07784.54960.01710.46040.3917-1.0189-0.0355-0.1055-0.18480.30020.01840.359-0.00880.00320.16210.04760.0475-30.434-12.678-18.281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 361:465 )A361 - 465
2X-RAY DIFFRACTION2( CHAIN B AND RESID 360:465 )B360 - 465

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