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- PDB-2cue: Solution structure of the homeobox domain of the human paired box... -

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Basic information

Entry
Database: PDB / ID: 2cue
TitleSolution structure of the homeobox domain of the human paired box protein Pax-6
ComponentsPaired box protein Pax6
KeywordsTRANSCRIPTION / homeobox domain / paired box protein / Pax6 / transcription factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pancreatic A cell development / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / commitment of neuronal cell to specific neuron type in forebrain / cerebral cortex regionalization / type B pancreatic cell differentiation / habenula development / forebrain dorsal/ventral pattern formation / cornea development in camera-type eye / regulation of timing of cell differentiation ...pancreatic A cell development / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / commitment of neuronal cell to specific neuron type in forebrain / cerebral cortex regionalization / type B pancreatic cell differentiation / habenula development / forebrain dorsal/ventral pattern formation / cornea development in camera-type eye / regulation of timing of cell differentiation / HMG box domain binding / iris morphogenesis / Formation of the anterior neural plate / regulation of asymmetric cell division / positive regulation of epithelial cell differentiation / embryonic camera-type eye morphogenesis / co-SMAD binding / lacrimal gland development / protein localization to organelle / pituitary gland development / ventral spinal cord development / sensory organ development / dorsal/ventral axis specification / eye photoreceptor cell development / neuron fate commitment / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / eye development / cell fate determination / astrocyte differentiation / lens development in camera-type eye / signal transduction involved in regulation of gene expression / negative regulation of neuroblast proliferation / smoothened signaling pathway / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / histone acetyltransferase binding / blood vessel development / forebrain development / R-SMAD binding / Regulation of gene expression in beta cells / establishment of mitotic spindle orientation / neuroblast proliferation / salivary gland morphogenesis / RNA polymerase II core promoter sequence-specific DNA binding / keratinocyte differentiation / visual perception / axon guidance / regulation of cell migration / cellular response to leukemia inhibitory factor / central nervous system development / animal organ morphogenesis / transcription coregulator binding / chromatin DNA binding / brain development / positive regulation of miRNA transcription / negative regulation of neurogenesis / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / neuron migration / negative regulation of epithelial cell proliferation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sequence-specific double-stranded DNA binding / glucose homeostasis / nervous system development / retina development in camera-type eye / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Paired box protein Pax-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsOhnishi, S. / Kigawa, T. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the homeobox domain of the human paired box protein Pax-6
Authors: Ohnishi, S. / Kigawa, T. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired box protein Pax6


Theoretical massNumber of molelcules
Total (without water)9,4241
Polymers9,4241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Paired box protein Pax6 / Oculorhombin / Aniridia / type II protein


Mass: 9424.414 Da / Num. of mol.: 1 / Fragment: homeobox domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PAX6 / Plasmid: P040712-10 / References: UniProt: P26367

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.50mM protein U-15N, 13C; 20mM d-TrisHCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert. P.structure solution
CYANA2.0.17Guntert. P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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