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Yorodumi- PDB-3kui: Crystal structure of C-terminal domain of PABPC1 in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3kui | ||||||
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Title | Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a | ||||||
Components |
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Keywords | PROTEIN BINDING / protein-protein complex / Acetylation / Alternative splicing / Cytoplasm / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome / GTP-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / translation release factor complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / translation release factor activity / regulation of translational termination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / translation release factor complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / translation release factor activity / regulation of translational termination / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / protein methylation / positive regulation of cytoplasmic translation / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Translation initiation complex formation / : / cell leading edge / Eukaryotic Translation Termination / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / translational termination / catalytic step 2 spliceosome / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / lamellipodium / ribonucleoprotein complex / translation / focal adhesion / GTPase activity / mRNA binding / GTP binding / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Molecular basis of eRF3 recognition by the MLLE domain of poly(A)-binding protein. Authors: Kozlov, G. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kui.cif.gz | 29.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kui.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kui_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 3kui_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 3kui_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 3kui_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kui ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kui | HTTPS FTP |
-Related structure data
Related structure data | 3kujC 1i2tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9421.909 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11940 |
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#2: Protein/peptide | Mass: 1736.004 Da / Num. of mol.: 1 / Fragment: PABPC1-binding region / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96GF2, UniProt: P15170*PLUS |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 2.1M ammonium sulfate, 0.2M sodium sulfate, 10mM zinc chloride, 0.1M sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 5, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 3570 / Num. obs: 3559 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.8 / Num. unique all: 235 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1I2T Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 46.44 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.34 Å /
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