[English] 日本語
Yorodumi- PDB-8p7g: Structural characterization of PHOX2B and its DNA interactions sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p7g | ||||||
---|---|---|---|---|---|---|---|
Title | Structural characterization of PHOX2B and its DNA interactions shed lights into the molecular basis of the + 7Ala variant pathogenicity in CCHS | ||||||
Components | Paired mesoderm homeobox protein 2B | ||||||
Keywords | PROTEIN BINDING / Transcription factor / Homeodomain / congenital central hypoventilation syndrome / polyAla expansions | ||||||
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 / noradrenergic neuron differentiation / cellular response to carbon dioxide / brainstem development / regulation of respiratory gaseous exchange by nervous system process / motor neuron migration / enteric nervous system development / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / glial cell differentiation / sympathetic nervous system development / type B pancreatic cell proliferation / cellular response to BMP stimulus / dopaminergic neuron differentiation / skeletal muscle cell differentiation / membrane depolarization / inner ear development / 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 / na | ||||||
Authors | Russo, L. / Diana, D. / Fattorusso, R. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Chem Sci / Year: 2024 Title: Structural characterization of PHOX2B and its DNA interaction shed light on the molecular basis of the +7Ala variant pathogenicity in CCHS. Authors: Diana, D. / Pirone, L. / Russo, L. / D'Abrosca, G. / Madheswaran, M. / Benfante, R. / Di Lascio, S. / Caldinelli, L. / Fornasari, D. / Acconcia, C. / Corvino, A. / Ventserova, N. / ...Authors: Diana, D. / Pirone, L. / Russo, L. / D'Abrosca, G. / Madheswaran, M. / Benfante, R. / Di Lascio, S. / Caldinelli, L. / Fornasari, D. / Acconcia, C. / Corvino, A. / Ventserova, N. / Pollegioni, L. / Isernia, C. / Di Gaetano, S. / Malgieri, G. / Pedone, E.M. / Fattorusso, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p7g.cif.gz | 425.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p7g.ent.gz | 356.6 KB | Display | PDB format |
PDBx/mmJSON format | 8p7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p7g_validation.pdf.gz | 476.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8p7g_full_validation.pdf.gz | 574.1 KB | Display | |
Data in XML | 8p7g_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 8p7g_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/8p7g ftp://data.pdbj.org/pub/pdb/validation_reports/p7/8p7g | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 7741.804 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q99453 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution Contents: 0.1 mM [U-13C; U-15N] Paired mesoderm homeobox protein 2B (Phox2B), 90% H2O/10% D2O Details: Homeodomain of Phox2B / Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O |
---|---|
Sample | Conc.: 0.1 mM / Component: Paired mesoderm homeobox protein 2B (Phox2B) / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 200 mM / Label: 15N13C_sample / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: na / Software ordinal: 2 | ||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 3000 / Conformers submitted total number: 20 |