[English] 日本語
Yorodumi- PDB-2yum: Solution structure of the Myb-like DNA-binding domain of human ZZ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yum | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the Myb-like DNA-binding domain of human ZZZ3 protein | ||||||
Components | Zinc finger ZZ-type-containing protein 3 | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information ATAC complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / methylated histone binding / histone reader activity / lysine-acetylated histone binding / mitotic spindle / chromatin organization ...ATAC complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / methylated histone binding / histone reader activity / lysine-acetylated histone binding / mitotic spindle / chromatin organization / HATs acetylate histones / regulation of cell cycle / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Abe, H. / Tochio, N. / Miyamoto, K. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the Myb-like DNA-binding domain of human ZZZ3 protein Authors: Abe, H. / Tochio, N. / Miyamoto, K. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE The sequence is based on Reference 2 in the database, ZZZ3_HUMAN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yum.cif.gz | 455.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yum.ent.gz | 382.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yum_validation.pdf.gz | 339.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yum_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 2yum_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 2yum_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/2yum ftp://data.pdbj.org/pub/pdb/validation_reports/yu/2yum | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8299.343 Da / Num. of mol.: 1 / Fragment: Myb-like DNA-binding domain, UNP residues 652-713 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: ZZZ3 / Plasmid: P050613-19 / References: UniProt: Q8IYH5 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.14mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
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 |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |