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Yorodumi- PDB-2dmd: Solution structure of the N-terminal C2H2 type zinc-binding domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmd | ||||||
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Title | Solution structure of the N-terminal C2H2 type zinc-binding domain of the Zinc finger protein 64, isoforms 1 and 2 | ||||||
Components | Zinc finger protein 64, isoforms 1 and 2 | ||||||
Keywords | TRANSCRIPTION / Zinc finger protein 338 / ZNF338 / Nuclear protein / DNA-binding / C2H2-type zinc finger / Structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information megasporocyte nucleus / mesenchymal cell differentiation / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the N-terminal C2H2 type zinc-binding domain of the Zinc finger protein 64, isoforms 1 and 2 Authors: Yoneyama, M. / Tochio, N. / 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 | 2dmd.cif.gz | 561.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmd.ent.gz | 468.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmd_validation.pdf.gz | 341.2 KB | Display | wwPDB validaton report |
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Full document | 2dmd_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 2dmd_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 2dmd_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmd ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmd | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 10492.898 Da / Num. of mol.: 1 / Fragment: C2H2-type zinc-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZFP64 / Plasmid: P050815-12 / Production host: Cell free synthesis / References: UniProt: Q9NPA5, UniProt: Q9NTW7*PLUS |
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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: 1.28mM C2H2 type zinc-binding domain U-15N, 13C; 20mM d-Tris HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM ZnCl2 + 1mM IDA; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / 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 / 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 |