+Open data
-Basic information
Entry | Database: PDB / ID: 2cqf | ||||||
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Title | Solution Structure of the Zinc-finger domain in LIN-28 | ||||||
Components | RNA-binding protein LIN-28 | ||||||
Keywords | TRANSCRIPTION / CCHC 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 negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding / Transcriptional regulation of pluripotent stem cells ...negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding / Transcriptional regulation of pluripotent stem cells / pre-miRNA processing / positive regulation of cytoplasmic translation / sequence-specific mRNA binding / miRNA binding / stem cell population maintenance / germ cell development / positive regulation of TOR signaling / rough endoplasmic reticulum / translation initiation factor binding / positive regulation of neuron differentiation / P-body / stem cell differentiation / cellular response to glucose stimulus / cytoplasmic stress granule / G-quadruplex RNA binding / negative regulation of translation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Someya, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the Zinc-finger domain in LIN-28 Authors: Someya, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, 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 | 2cqf.cif.gz | 337.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cqf.ent.gz | 290.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/2cqf ftp://data.pdbj.org/pub/pdb/validation_reports/cq/2cqf | HTTPS FTP |
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-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: 6438.213 Da / Num. of mol.: 1 / Fragment: Zinc-finger (130-192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: LIN28 / Plasmid: P041101-01 / References: UniProt: Q9H9Z2 |
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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: 1.13mM PROTEIN U-15N,13C; 20mM d-Tris-HCL(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.25mM ZnCl2+1mM IDA; 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 lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |