+Open data
-Basic information
Entry | Database: PDB / ID: 4c8q | ||||||
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Title | Crystal structure of the yeast Lsm1-7-Pat1 complex | ||||||
Components |
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Keywords | TRANSCRIPTION / MRNA DECAPPING / SM FOLD / MRNA DEGRADATION | ||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / U4/U6 snRNP / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / regulation of translational initiation / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal snRNP assembly / U6 snRNA binding / maturation of SSU-rRNA / 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 / ribonucleoprotein complex / 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 / MOLECULAR REPLACEMENT / Resolution: 3.698 Å | ||||||
Authors | Sharif, H. / Conti, E. | ||||||
Citation | Journal: Cell Rep. / Year: 2013 Title: Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic Mrna Turnover Authors: Sharif, H. / Conti, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c8q.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c8q.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/4c8q ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c8q | HTTPS FTP |
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-Related structure data
Related structure data | 4c92SC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules AH
#1: Protein | Mass: 11935.651 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P47017 |
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#8: Protein | Mass: 37934.699 Da / Num. of mol.: 1 / Fragment: RESIDUES 456-783 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25644 |
-U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN ... , 6 types, 6 molecules BCDEFG
#2: Protein | Mass: 12216.880 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38203 |
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#3: Protein | Mass: 10039.262 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P57743 |
#4: Protein | Mass: 13035.543 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40070 |
#5: Protein | Mass: 10432.954 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40089 |
#6: Protein | Mass: 9406.579 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-86 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q06406 |
#7: Protein | Mass: 13027.045 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53905 |
-Non-polymers , 1 types, 2 molecules
#9: Chemical |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.39 % Description: CHIMERIC MODEL WAS MADE FOR MOLECULAR REPLACEMENT |
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Crystal grow | Details: 100 MM HEPES PH 7.0, 20% MPD, 10 MM HEXAMINE COBALT(III) CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→84.68 Å / Num. obs: 36441 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 133.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.7→3.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C92 Resolution: 3.698→43.42 Å / SU ML: 0.67 / σ(F): 39.43 / Phase error: 31.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 129.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.698→43.42 Å
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Refine LS restraints |
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LS refinement shell |
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