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- PDB-8p7g: Structural characterization of PHOX2B and its DNA interactions sh... -

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Basic information

Entry
Database: PDB / ID: 8p7g
TitleStructural characterization of PHOX2B and its DNA interactions shed lights into the molecular basis of the + 7Ala variant pathogenicity in CCHS
ComponentsPaired mesoderm homeobox protein 2B
KeywordsPROTEIN BINDING / Transcription factor / Homeodomain / congenital central hypoventilation syndrome / polyAla expansions
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 / cell differentiation in hindbrain / noradrenergic neuron development / 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 / cell differentiation in hindbrain / noradrenergic neuron development / respiratory system development / autonomic nervous system development / hindbrain tangential cell migration / noradrenergic neuron differentiation / cellular response to carbon dioxide / brainstem development / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / enteric nervous system development / regulation of respiratory gaseous exchange by nervous system process / sympathetic nervous system development / glial cell differentiation / cellular response to BMP stimulus / dopaminergic neuron differentiation / type B pancreatic cell proliferation / negative regulation of neuron differentiation / inner ear development / skeletal muscle cell differentiation / membrane depolarization / 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 / na
AuthorsRusso, L. / Diana, D. / Fattorusso, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionMay 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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)7,7421
Polymers7,7421
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 / 3000structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

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


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HNHA

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Sample preparation

DetailsType: 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
SampleConc.: 0.1 mM / Component: Paired mesoderm homeobox protein 2B (Phox2B) / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 200 mM / Label: 15N13C_sample / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CARAKeller and Wuthrichpeak picking
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 20

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