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Yorodumi- PDB-2djn: The solution structure of the homeobox domain of human Homeobox p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2djn | ||||||
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Title | The solution structure of the homeobox domain of human Homeobox protein DLX-5 | ||||||
Components | Homeobox protein DLX-5 | ||||||
Keywords | TRANSCRIPTION / homeobox / DLX5 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information interneuron axon guidance / olfactory pit development / HMG box domain binding / olfactory bulb interneuron differentiation / anatomical structure formation involved in morphogenesis / Specification of the neural plate border / endochondral ossification / face morphogenesis / embryonic limb morphogenesis / inner ear morphogenesis ...interneuron axon guidance / olfactory pit development / HMG box domain binding / olfactory bulb interneuron differentiation / anatomical structure formation involved in morphogenesis / Specification of the neural plate border / endochondral ossification / face morphogenesis / embryonic limb morphogenesis / inner ear morphogenesis / roof of mouth development / BMP signaling pathway / epithelial cell differentiation / positive regulation of epithelial cell proliferation / skeletal system development / osteoblast differentiation / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Sasagawa, A. / Ohnishi, S. / Tochio, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The solution structure of the homeobox domain of human Homeobox protein DLX-5 Authors: Sasagawa, A. / Ohnishi, S. / Tochio, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2djn.cif.gz | 428.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2djn.ent.gz | 360.6 KB | Display | PDB format |
PDBx/mmJSON format | 2djn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/2djn ftp://data.pdbj.org/pub/pdb/validation_reports/dj/2djn | 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: 7741.847 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: DLX5 / Plasmid: P050509-13 / Production host: Cell free synthesis / References: UniProt: P56178 |
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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: 1.35mM homeobox domain U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / 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 / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy, fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |