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- PDB-8ptl: human PHOX2B C-terminal domain including the polyA fragment at 278K -

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Basic information

Entry
Database: PDB / ID: 8ptl
Titlehuman PHOX2B C-terminal domain including the polyA fragment at 278K
ComponentsPaired mesoderm homeobox protein 2B
KeywordsTRANSCRIPTION / CCHS / polyA / homorepeat / trinucleotide repeat expansion
Function / homology
Function and homology information


medullary reticular formation development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / autonomic nervous system development / hindbrain tangential cell migration ...medullary reticular formation development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / autonomic nervous system development / hindbrain tangential cell migration / cellular response to carbon dioxide / noradrenergic neuron differentiation / brainstem development / regulation of respiratory gaseous exchange by nervous system process / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / enteric nervous system development / glial cell differentiation / sympathetic nervous system development / cellular response to BMP stimulus / type B pancreatic cell proliferation / dopaminergic neuron differentiation / skeletal muscle cell differentiation / inner ear development / membrane depolarization / negative regulation of neuron differentiation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of neuron differentiation / response to activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Paired mesoderm homeobox protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAnton, R. / Trevino, M.A. / Pantoja-Uceda, D. / Felix, S. / Babu, M. / Cabrita, E.J. / Zweckstetter, M. / Tinnefeld, P. / Vera, A.M. / Oroz, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109276RA-I00 Spain
CitationJournal: Nat Commun / Year: 2024
Title: Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions.
Authors: Anton, R. / Trevino, M.A. / Pantoja-Uceda, D. / Felix, S. / Babu, M. / Cabrita, E.J. / Zweckstetter, M. / Tinnefeld, P. / Vera, A.M. / Oroz, J.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired mesoderm homeobox protein 2B


Theoretical massNumber of molelcules
Total (without water)7,5351
Polymers7,5351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Paired mesoderm homeobox protein 2B / Neuroblastoma Phox / NBPhox / PHOX2B homeodomain protein / Paired-like homeobox 2B


Mass: 7535.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHOX2B, PMX2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star (DE3) / References: UniProt: Q99453

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
161isotropic13D CBCA(CO)NH
171isotropic13D H(CCO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D HN(CO)CA
1101isotropic13D HNCA
1111isotropic13D HNCO
1121isotropic13D HNHA

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] human PHOX2B, 5 mM potassium phosphate, 10 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.05 mM DSS, 0.03 % v/v sodium azide, 90% H2O/10% D2O
Details: 0.5 mM sample in 5 mM KPi/10 mM NaCl/2 mM beta-mercaptoethanol [pH 6.8]
Label: 15N/13C_XS20 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhuman PHOX2B[U-13C; U-15N]1
5 mMpotassium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
2 mMbeta-mercaptoethanolnatural abundance1
0.05 mMDSSnatural abundance1
0.03 % v/vsodium azidenatural abundance1
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.8 / Pressure: AMBIENT atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.1.2Bruker Biospincollection
NMRFAM-SPARKYLee, W.; Tonelli, M.; Markley, J. L. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 2015, 31 (8), 1325-1327. DOI: 10.1093/bioinformatics/btu830.chemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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