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Yorodumi- PDB-8ptl: human PHOX2B C-terminal domain including the polyA fragment at 278K -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ptl | ||||||
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Title | human PHOX2B C-terminal domain including the polyA fragment at 278K | ||||||
Components | Paired mesoderm homeobox protein 2B | ||||||
Keywords | TRANSCRIPTION / CCHS / polyA / homorepeat / trinucleotide repeat expansion | ||||||
Function / homology | Function and homology information medullary reticular formation development / autonomic nervous system 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 / hindbrain tangential cell migration ...medullary reticular formation development / autonomic nervous system 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 / hindbrain tangential cell migration / cellular response to carbon dioxide / noradrenergic neuron differentiation / brainstem development / motor neuron migration / regulation of respiratory gaseous exchange by nervous system process / sympathetic ganglion development / enteric nervous system development / neural crest cell migration involved in autonomic nervous system development / glial cell differentiation / type B pancreatic cell proliferation / sympathetic nervous system development / cellular response to BMP stimulus / 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 / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
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. | ||||||
Funding support | Spain, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ptl.cif.gz | 408.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ptl.ent.gz | 349.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ptl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/8ptl ftp://data.pdbj.org/pub/pdb/validation_reports/pt/8ptl | HTTPS FTP |
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-Related structure data
Related structure data | 8puiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 mM / Label: conditions_1 / pH: 6.8 / Pressure: AMBIENT atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |