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Yorodumi- PDB-4n0a: Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n0a | ||||||
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Title | Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Decapping activator | ||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / U4/U6 snRNP / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / regulation of translational initiation / tRNA processing ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / U4/U6 snRNP / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / regulation of translational initiation / tRNA processing / precatalytic spliceosome / negative regulation of translational initiation / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / kinetochore / mRNA processing / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / cell cycle / cell division / mRNA binding / chromatin binding / nucleolus / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å | ||||||
Authors | Wu, D.H. | ||||||
Citation | Journal: Cell Res. / Year: 2014 Title: Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation Authors: Wu, D. / Muhlrad, D. / Bowler, M.W. / Jiang, S. / Liu, Z. / Parker, R. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n0a.cif.gz | 307.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n0a.ent.gz | 248.1 KB | Display | PDB format |
PDBx/mmJSON format | 4n0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0a ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10039.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743 #2: Protein | Mass: 12796.582 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203 #3: Protein | Mass: 43190.473 Da / Num. of mol.: 3 / Fragment: UNP residues 423-796 / Mutation: D688V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MRT1, PAT1, YCR077C, YCR77C / Production host: Escherichia coli (E. coli) / References: UniProt: P25644 #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: 4.66 Å3/Da / Density % sol: 73.62 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris, 12% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072, 1.2553, 1.2557, 1.2427 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2010 | |||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.15→19.9 Å / Num. all: 65278 / Num. obs: 65011 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | |||||||||||||||
Reflection shell | Resolution: 3.15→3.2621 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.15→19.884 Å / SU ML: 0.45 / σ(F): 1 / Phase error: 38.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.001 Å2 / ksol: 0.272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.15→19.884 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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