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Yorodumi- PDB-2cue: Solution structure of the homeobox domain of the human paired box... -
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-Basic information
Entry | Database: PDB / ID: 2cue | ||||||
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Title | Solution structure of the homeobox domain of the human paired box protein Pax-6 | ||||||
Components | Paired box protein Pax6Pax genes | ||||||
Keywords | TRANSCRIPTION / 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 / rhombomere morphogenesis / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / learned vocalization behavior or vocal learning / positive regulation of glutamatergic neuron differentiation / sensory neuron migration / commitment of neuronal cell to specific neuron type in forebrain / type B pancreatic cell differentiation / cerebral cortex regionalization ...pancreatic A cell development / rhombomere morphogenesis / oligodendrocyte cell fate specification / forebrain-midbrain boundary formation / learned vocalization behavior or vocal learning / positive regulation of glutamatergic neuron differentiation / sensory neuron migration / commitment of neuronal cell to specific neuron type in forebrain / type B pancreatic cell differentiation / cerebral cortex regionalization / olfactory bulb mitral cell layer development / habenula development / forebrain dorsal/ventral pattern formation / cornea development in camera-type eye / regulation of timing of cell differentiation / HMG box domain binding / positive regulation of cell fate specification / interkinetic nuclear migration / iris morphogenesis / Formation of the anterior neural plate / positive regulation of epithelial cell differentiation / regulation of asymmetric cell division / embryonic camera-type eye morphogenesis / ventral spinal cord development / lacrimal gland development / co-SMAD binding / protein localization to organelle / pituitary gland development / dorsal/ventral axis specification / insulin metabolic process / eye photoreceptor cell development / positive regulation of core promoter binding / neuron fate commitment / eye development / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / positive regulation of neuron migration / signal transduction involved in regulation of gene expression / cell fate determination / anatomical structure development / astrocyte differentiation / cellular response to fibroblast growth factor stimulus / : / lens development in camera-type eye / neural crest cell migration / negative regulation of neuroblast proliferation / histone acetyltransferase binding / : / smoothened signaling pathway / positive regulation of neuroblast proliferation / regulation of neuron projection development / blood vessel development / minor groove of adenine-thymine-rich DNA binding / establishment of mitotic spindle orientation / R-SMAD binding / Regulation of gene expression in beta cells / neuroblast proliferation / negative regulation of neuron differentiation / RNA polymerase II core promoter sequence-specific DNA binding / salivary gland morphogenesis / keratinocyte differentiation / visual perception / cellular response to leukemia inhibitory factor / cerebellum development / negative regulation of protein phosphorylation / central nervous system development / axon guidance / transcription coregulator binding / cellular response to glucose stimulus / animal organ morphogenesis / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / positive regulation of miRNA transcription / negative regulation of neurogenesis / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to prostaglandin E stimulus / cellular response to insulin stimulus / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / sequence-specific double-stranded DNA binding / glucose homeostasis / retina development in camera-type eye / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Ohnishi, S. / Kigawa, T. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: 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 |
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Remark 650 | HELIX Determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cue.cif.gz | 504.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cue.ent.gz | 439.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cue ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cue | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |