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Yorodumi- PDB-2ecb: The solution structure of the third homeobox domain of human zinc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ecb | |||||||||
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Title | The solution structure of the third homeobox domain of human zinc fingers and homeoboxes protein | |||||||||
Components | Zinc fingers and homeoboxes protein 1 | |||||||||
Keywords | TRANSCRIPTION / homeobox domain / ZINC FINGERS AND HOMEOBOXES PROTEIN / transcription factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm ...cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained simulated annealing | |||||||||
Authors | Ohnishi, S. / Tochio, N. / Sasagawa, A. / 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 third homeobox domain of human Zinc fingers and homeoboxes protein Authors: Ohnishi, S. / Tochio, N. / Sasagawa, A. / 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 | 2ecb.cif.gz | 530.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ecb.ent.gz | 448.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ecb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ecb_validation.pdf.gz | 343.2 KB | Display | wwPDB validaton report |
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Full document | 2ecb_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 2ecb_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 2ecb_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2ecb ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2ecb | 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: 9823.867 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: ZHX1 / Plasmid: P050404-21 / References: UniProt: Q9UKY1 |
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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: 1.14MM 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, restrained simulated annealing 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 |