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Yorodumi- PDB-2cuf: Solution structure of the homeobox domain of the human hypothetic... -
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-Basic information
Entry | Database: PDB / ID: 2cuf | ||||||
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Title | Solution structure of the homeobox domain of the human hypothetical protein FLJ21616 | ||||||
Components | FLJ21616 protein | ||||||
Keywords | DNA BINDING PROTEIN / homeobox domain / FLJ21616 / hepatocyte transcription factor / structural genomics / loop insertion / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information chromosome, telomeric region => GO:0000781 / regulation of telomerase activity / chromatin => GO:0000785 / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / Cajal body / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / PML body ...chromosome, telomeric region => GO:0000781 / regulation of telomerase activity / chromatin => GO:0000785 / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / Cajal body / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromosome, telomeric region / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / centrosome / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Ohnishi, S. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the homeobox domain of the human hypothetical protein FLJ21616 Authors: Ohnishi, S. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX Determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cuf.cif.gz | 577 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cuf.ent.gz | 486.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cuf_validation.pdf.gz | 340.3 KB | Display | wwPDB validaton report |
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Full document | 2cuf_full_validation.pdf.gz | 466.9 KB | Display | |
Data in XML | 2cuf_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 2cuf_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cuf ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cuf | 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: 10659.966 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: FLJ21616 / Plasmid: P041004-01 / References: UniProt: Q9H701, UniProt: Q6NT76*PLUS |
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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: 1.40mM protein U-15N, 13C; 20mM d-TrisHCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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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 |
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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: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |