[English] 日本語
Yorodumi- PDB-4a54: Structural basis of the Dcp1:Dcp2 mRNA decapping complex activati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a54 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis of the Dcp1:Dcp2 mRNA decapping complex activation by Edc3 and Scd6 | ||||||
Components |
| ||||||
Keywords | RNA BINDING PROTEIN/HYDROLASE / RNA BINDING PROTEIN-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / molecular condensate scaffold activity / P-body / cytoplasmic stress granule / mRNA processing / manganese ion binding / single-stranded RNA binding / mRNA binding / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SCHIZOSACCHAROMYCES POMBE (fission yeast) | ||||||
Method | SOLUTION NMR / XPLOR | ||||||
Authors | Fromm, S.A. / Truffault, V. / Kamenz, J. / Braun, J.E. / Hoffmann, N.A. / Izaurralde, E. / Sprangers, R. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: The Structural Basis of Edc3- and Scd6-Mediated Activation of the Dcp1:Dcp2 Mrna Decapping Complex. Authors: Fromm, S.A. / Truffault, V. / Kamenz, J. / Braun, J.E. / Hoffmann, N.A. / Izaurralde, E. / Sprangers, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4a54.cif.gz | 961.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4a54.ent.gz | 812.1 KB | Display | PDB format |
PDBx/mmJSON format | 4a54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a54_validation.pdf.gz | 475.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4a54_full_validation.pdf.gz | 731.8 KB | Display | |
Data in XML | 4a54_validation.xml.gz | 64 KB | Display | |
Data in CIF | 4a54_validation.cif.gz | 87.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a54 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a54 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10601.993 Da / Num. of mol.: 1 / Fragment: LSM, RESIDUES 1-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O94752 |
---|---|
#2: Protein | Mass: 5342.786 Da / Num. of mol.: 1 / Fragment: HLM1, RESIDUES 242-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O13828, Hydrolases |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: NOESY |
NMR details | Text: NONE |
-Sample preparation
Details | Contents: 90% WATER/10% D2O |
---|---|
Sample conditions | Ionic strength: 125 mM / pH: 7.3 / Pressure: 1.0 atm / Temperature: 303.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: XPLOR / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 22 |