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Yorodumi- PDB-3kut: Crystal structure of the MLLE domain of poly(A)-binding protein i... -
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-Basic information
Entry | Database: PDB / ID: 3kut | ||||||
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Title | Crystal structure of the MLLE domain of poly(A)-binding protein in complex with the binding region of Paip2 | ||||||
Components |
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Keywords | PROTEIN BINDING / protein-protein complex / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome | ||||||
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 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / regulation of long-term synaptic potentiation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / cell leading edge / 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) / translation repressor activity / negative regulation of translational initiation / catalytic step 2 spliceosome / mRNA regulatory element binding translation repressor activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / memory / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / lamellipodium / spermatogenesis / negative regulation of translation / translation / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Molecular Determinants of PAM2 Recognition by the MLLE Domain of Poly(A)-Binding Protein. Authors: Kozlov, G. / Menade, M. / Rosenauer, A. / Nguyen, L. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kut.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kut.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 3kut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kut_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 3kut_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 3kut_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 3kut_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kut ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kut | HTTPS FTP |
-Related structure data
Related structure data | 3kurC 3kusC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9421.909 Da / Num. of mol.: 2 / 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 #2: Protein/peptide | Mass: 1777.951 Da / Num. of mol.: 2 / Fragment: PABPC1-binding region / Mutation: K116A / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6FID7, UniProt: Q9BPZ3*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.25M ammonium sulfate, 0.2M KBr, 0.1 M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.995 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.995 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 23114 / Num. obs: 22328 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1593 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1I2T Resolution: 1.5→47.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.525 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.764 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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