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- PDB-2k7s: Human ARNT C-Terminal PAS Domain, 3 Residue IB slip -

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Basic information

Entry
Database: PDB / ID: 2k7s
TitleHuman ARNT C-Terminal PAS Domain, 3 Residue IB slip
ComponentsAryl hydrocarbon receptor nuclear translocator
KeywordsTRANSCRIPTION / ARNT PAS-B / Beta-strand Slip / PAS domain / Activator / Alternative splicing / DNA-binding / Nucleus / Polymorphism / Transcription regulation
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)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
AuthorsEvans, M.R. / Card, P.B. / Gardner, K.H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space
Authors: Evans, M.R. / Card, P.B. / Gardner, K.H.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Structural Basis of ARNT PAS-B Dimerization: Use of a Common Beta-sheet Interface for Hetero- and Homodimerization
Authors: Card, P.B. / Erbel, P.J.A. / Gardner, K.H.
History
DepositionAug 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator


Theoretical massNumber of molelcules
Total (without water)13,7991
Polymers13,7991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1 beta / HIF-1 beta


Mass: 13799.488 Da / Num. of mol.: 1 / Fragment: ARNT PAS-B / Mutation: F444Q, F446A, Y456T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27540

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1612D 1H-1H TOCSY
1712D 1H-1H NOESY
1813D 1H-13C NOESY
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 900 uM [U-98% 13C; U-98% 15N] ARNT PAS-B Slipped IB Strand, 50 mM TRIS, 17 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
900 uMARNT PAS-B Slipped IB Strand[U-98% 13C; U-98% 15N]1
50 mMTRIS1
17 mMsodium chloride1
5 mMDTT1
Sample conditionsIonic strength: 17 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2Johnson, One Moon Scientificpeak picking
NMRView5.2.2Johnson, One Moon Scientificdata analysis
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
ARIA2.1Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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