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Yorodumi- PDB-6ppv: Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ppv | ||||||
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Title | Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / RNA metabolic process / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / : / P-body assembly ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / chromosome, telomeric repeat region / RNA metabolic process / Lsm1-7-Pat1 complex / U6 snRNP / RNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / : / P-body assembly / spliceosomal tri-snRNP complex / sno(s)RNA-containing ribonucleoprotein complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / telomerase holoenzyme complex / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / telomerase holoenzyme complex assembly / RNA folding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / P-body / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / rRNA processing / ribonucleoprotein complex / chromatin binding / nucleolus / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Montemayor, E.J. / Butcher, S.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rna / Year: 2020 Title: Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes. Authors: Montemayor, E.J. / Virta, J.M. / Hayes, S.M. / Nomura, Y. / Brow, D.A. / Butcher, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ppv.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ppv.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ppv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/6ppv ftp://data.pdbj.org/pub/pdb/validation_reports/pp/6ppv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-U6 snRNA-associated Sm-like protein ... , 5 types, 5 molecules ABEFG
#1: Protein | Mass: 9754.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm1, SPBC3D6.08c / Production host: Escherichia coli (E. coli) / References: UniProt: P87173 |
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#2: Protein | Mass: 11003.798 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm2, SPCC1620.01c / Production host: Escherichia coli (E. coli) / References: UniProt: O94408 |
#5: Protein | Mass: 8860.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm5, SPBC20F10.09 / Production host: Escherichia coli (E. coli) / References: UniProt: O42978 |
#6: Protein | Mass: 8489.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm6, SPAC2F3.17c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUI1 |
#7: Protein | Mass: 12488.179 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm7, SPCC285.12 / Production host: Escherichia coli (E. coli) / References: UniProt: O74499 |
-Probable U6 snRNA-associated Sm-like protein ... , 2 types, 2 molecules CD
#3: Protein | Mass: 10824.278 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm3, SPBC9B6.05c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y7M4 |
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#4: Protein | Mass: 15007.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: lsm4, SPBC30D10.06 / Production host: Escherichia coli (E. coli) / References: UniProt: O14352 |
-RNA chain / Non-polymers , 2 types, 191 molecules H
#8: RNA chain | Mass: 1854.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium tartrate, 20 mM sodium oxamate, 100 mM sodium HEPES base, 100 mM MOPS acid, 10 % PEG 8,000, 20 % ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→98.7 Å / Num. obs: 52874 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 45.4 Å2 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.05→2.11 Å / Num. unique obs: 4047 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42.07 Å / SU ML: 0.3426 / Cross valid method: FREE R-VALUE / σ(F): 0.42 / Phase error: 29.1337
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→42.07 Å
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Refine LS restraints |
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LS refinement shell |
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