[English] 日本語
Yorodumi- PDB-2mkk: Structural model of tandem RRM domains of cytoplasmic polyadenyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mkk | ||||||
---|---|---|---|---|---|---|---|
Title | Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA | ||||||
Components |
| ||||||
Keywords | TRANSLATION REGULATOR/RNA / CPEB1 / RNA recognition motif (RRM) / Cytoplasmic polyadenylation / Protein-RNA Interaction / Translation regulation / TRANSLATION REGULATOR-RNA complex | ||||||
Function / homology | Function and homology information : / regulation of mRNA 3'-end processing / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / negative regulation of cytoplasmic translation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cellular response to amino acid stimulus / P-body / mRNA processing ...: / regulation of mRNA 3'-end processing / translation factor activity, RNA binding / mRNA 3'-UTR AU-rich region binding / negative regulation of cytoplasmic translation / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / cellular response to amino acid stimulus / P-body / mRNA processing / cellular response to insulin stimulus / ribosome binding / cellular response to hypoxia / postsynaptic density / neuron projection / synapse / dendrite / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model2 | ||||||
Authors | Afroz, T. / Skrisovska, L. / Belloc, E. / Boixet, J.G. / Mendez, R. / Allain, F.H.-T. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins Authors: Afroz, T. / Skrisovska, L. / Belloc, E. / Guillen-Boixet, J. / Mendez, R. / Allain, F.H.-T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mkk.cif.gz | 691.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mkk.ent.gz | 576.6 KB | Display | PDB format |
PDBx/mmJSON format | 2mkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mkk_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2mkk_full_validation.pdf.gz | 541.9 KB | Display | |
Data in XML | 2mkk_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 2mkk_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/2mkk ftp://data.pdbj.org/pub/pdb/validation_reports/mk/2mkk | HTTPS FTP |
-Related structure data
Related structure data | 2mkeC 2mkhC 2mkiC 2mkjC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 23930.580 Da / Num. of mol.: 1 / Fragment: UNP residues 219-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB1, CPEB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZB8 |
---|---|
#2: RNA chain | Mass: 1508.912 Da / Num. of mol.: 1 / Source method: obtained synthetically |
Sequence details | THIS PROTEIN SEQUENCE IS ISOFORM 4 OF CPEB1_HUMAN. |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 0.15 / pH: 6.5 / Pressure: ambient atm / Temperature: 313 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 10 / Representative conformer: 2 |