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Yorodumi- PDB-2dmi: Solution structure of the first and the second zf-C2H2 like domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmi | ||||||
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Title | Solution structure of the first and the second zf-C2H2 like domains of human Teashirt homolog 3 | ||||||
Components | Teashirt homolog 3 | ||||||
Keywords | TRANSCRIPTION / Zinc finger protein 537 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of respiratory gaseous exchange by nervous system process / multicellular organism development / chromatin => GO:0000785 / positive regulation of synaptic transmission, glutamatergic / long-term synaptic potentiation / growth cone / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II ...regulation of respiratory gaseous exchange by nervous system process / multicellular organism development / chromatin => GO:0000785 / positive regulation of synaptic transmission, glutamatergic / long-term synaptic potentiation / growth cone / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first and the second zf-C2H2 like domains of human Teashirt homolog 3 Authors: Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dmi.cif.gz | 700.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmi.ent.gz | 585.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmi_validation.pdf.gz | 342.5 KB | Display | wwPDB validaton report |
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Full document | 2dmi_full_validation.pdf.gz | 494.2 KB | Display | |
Data in XML | 2dmi_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 2dmi_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmi ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmi | 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: 12914.487 Da / Num. of mol.: 1 / Fragment: zf-C2H2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: ZNF537 / Plasmid: P050905-02 / Production host: Cell free synthesis / References: UniProt: Q63HK5 |
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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: 1.19mM; 20mM Nad-Mal(6.0),100mM NaCl,0.1mM DTT,0.02%NaN3,0.05mM ZnCl2,1mM NTA Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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 | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |