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Yorodumi- PDB-1ifw: SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEI... -
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-Basic information
Entry | Database: PDB / ID: 1ifw | ||||||
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Title | SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF POLY(A) BINDING PROTEIN FROM SACCHAROMYCES CEREVISIAE | ||||||
Components | POLYADENYLATE-BINDING PROTEIN, CYTOPLASMIC AND NUCLEAR | ||||||
Keywords | RNA BINDING PROTEIN / all-helical domain | ||||||
Function / homology | Function and homology information regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / poly(A) binding / poly(U) RNA binding / regulation of translational initiation / Translation initiation complex formation / intracellular non-membrane-bounded organelle / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression ...regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / poly(A) binding / poly(U) RNA binding / regulation of translational initiation / Translation initiation complex formation / intracellular non-membrane-bounded organelle / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / mRNA transport / molecular condensate scaffold activity / mRNA 3'-UTR binding / promoter-specific chromatin binding / mRNA processing / cytoplasmic stress granule / ribosome / ribonucleoprotein complex / mRNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Sprules, T. / Ekiel, I. / Gehring, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Solution structure of the orphan PABC domain from Saccharomyces cerevisiae poly(A)-binding protein. Authors: Kozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Trempe, J.F. / Ekiel, I. / Sprules, T. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifw.cif.gz | 820.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifw.ent.gz | 721.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ifw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifw ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10445.410 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (490-576) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PAB1 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: P04147 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using standard triple-resonance and homonuclear techniques. The N-terminal sequence GPLGS is a cloning artifact. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 0.2 / pH: 6.3 / Pressure: ambient / Temperature: 303 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on 972 NOE distance constraints, 69 dihedral angles constraints and 40 hydrogen bonds. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 30 |