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Yorodumi- PDB-2ej4: Functional and structural basis of nuclear localization signal in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ej4 | ||||||
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Title | Functional and structural basis of nuclear localization signal in ZIC3 zinc finger domain: a role of conserved tryptophan residue in the zinc finger domain | ||||||
Components | Zinc finger protein ZIC 3 | ||||||
Keywords | GENE REGULATION / zf-C2H2 domain / zinc binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information central nervous system segmentation / determination of left/right asymmetry in nervous system / determination of pancreatic left/right asymmetry / determination of digestive tract left/right asymmetry / determination of liver left/right asymmetry / atrial cardiac muscle tissue development / neural plate development / primitive streak formation / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / left/right axis specification ...central nervous system segmentation / determination of left/right asymmetry in nervous system / determination of pancreatic left/right asymmetry / determination of digestive tract left/right asymmetry / determination of liver left/right asymmetry / atrial cardiac muscle tissue development / neural plate development / primitive streak formation / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / left/right axis specification / germ-line stem cell population maintenance / limb morphogenesis / Transcriptional regulation of pluripotent stem cells / cranial skeletal system development / paraxial mesoderm development / olfactory bulb development / embryonic pattern specification / axial mesoderm development / outer ear morphogenesis / determination of left/right symmetry / smoothened signaling pathway / heart looping / face development / skeletal system development / central nervous system development / stem cell differentiation / hippocampus development / lung development / mRNA transcription by RNA polymerase II / neuron differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Functional and structural basis of nuclear localization signal in ZIC3 zinc finger domain: a role of conserved tryptophan residue in the zinc finger domain Authors: Hatayama, M. / Tomizawa, T. / Bouvagnet, P. / Yokoyama, S. / Mikoshiba, K. / Kigawa, T. / Aruga, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ej4.cif.gz | 570 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ej4.ent.gz | 473.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ej4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ej4_validation.pdf.gz | 344.2 KB | Display | wwPDB validaton report |
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Full document | 2ej4_full_validation.pdf.gz | 501.8 KB | Display | |
Data in XML | 2ej4_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 2ej4_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/2ej4 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/2ej4 | HTTPS FTP |
-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: 10631.933 Da / Num. of mol.: 1 / Fragment: ZIC3_C2H2-12 domain, UNP residues 245-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZIC3 / Plasmid: P050815-02 / References: UniProt: O60481 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.13mM ZIC3_C2H2-12 U-15N,13C; 20mM d-malonic acid-NaOH(pH6.0); 100mM NaCl; 0.1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM NTA; 90% H2O,10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 296 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: structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |