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- PDB-4eq1: Crystal Structure of the ARNT PAS-B homodimer -

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Basic information

Entry
Database: PDB / ID: 4eq1
TitleCrystal Structure of the ARNT PAS-B homodimer
ComponentsAryl hydrocarbon receptor nuclear translocator
KeywordsTRANSCRIPTION / Per-ARNT-Sim / transcription regulation / homodimer / transcription factor / DNA-binding / HIF1 / HIF2 / Ahr
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 / 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. ...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 / 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. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGardner, K.H. / Key, J.M.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Regulating the ARNT/TACC3 Axis: Multiple Approaches to Manipulating Protein/Protein Interactions with Small Molecules.
Authors: Guo, Y. / Partch, C.L. / Key, J. / Card, P.B. / Pashkov, V. / Patel, A. / Bruick, R.K. / Wurdak, H. / Gardner, K.H.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)26,1003
Polymers25,7012
Non-polymers3981
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-3 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.315, 61.678, 55.514
Angle α, β, γ (deg.)90.000, 124.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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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: 12850.557 Da / Num. of mol.: 2 / Fragment: PAS-B domain (UNP residues 357-464)
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-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Ammonium Sulfate, 3% PEG400, 1% PEI, 50mM Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: CUSTOM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.6→24.047 Å / Num. obs: 34166 / % possible obs: 99.71 % / Redundancy: 4.55 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 38.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1P chain A

3f1p


Resolution: 1.6→24.047 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8383 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1740 5.09 %
Rwork0.2015 --
obs0.2028 34166 99.71 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.041 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 102.28 Å2 / Biso mean: 22.0151 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.1081 Å2-0 Å2-0.1191 Å2
2--0.0709 Å20 Å2
3---0.0371 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 14 206 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141885
X-RAY DIFFRACTIONf_angle_d1.4482551
X-RAY DIFFRACTIONf_chiral_restr0.086275
X-RAY DIFFRACTIONf_plane_restr0.008330
X-RAY DIFFRACTIONf_dihedral_angle_d16.149706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64710.30111340.245427062840100
1.6471-1.70020.24171280.22726832811100
1.7002-1.7610.28431430.21826882831100
1.761-1.83150.28041520.211726762828100
1.8315-1.91480.24041350.202527292864100
1.9148-2.01570.22251610.198826622823100
2.0157-2.14190.21351440.202527132857100
2.1419-2.30720.23881470.205826902837100
2.3072-2.53910.21871490.194527052854100
2.5391-2.9060.24731610.196226862847100
2.906-3.65920.20121560.188927142870100
3.6592-24.04940.20611300.20172774290499

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