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- PDB-6ppq: Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' adenosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ppq | ||||||
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Title | Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' adenosine | ||||||
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![]() | RNA BINDING PROTEIN/RNA / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() 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 / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / poly(U) RNA binding / U2 snRNP / tRNA processing / U2-type prespliceosome / telomerase holoenzyme complex assembly / precatalytic spliceosome / nuclear-transcribed mRNA catabolic process / RNA folding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / mRNA processing / rRNA processing / ribonucleoprotein complex / chromatin binding / nucleolus / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Montemayor, E.J. / Butcher, S.E. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253 KB | Display | ![]() |
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PDB format | ![]() | 189.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm1, SPBC3D6.08c / Production host: ![]() ![]() |
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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.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm2, SPCC1620.01c / Production host: ![]() ![]() |
#5: Protein | Mass: 8860.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm5, SPBC20F10.09 / Production host: ![]() ![]() |
#6: Protein | Mass: 8489.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm6, SPAC2F3.17c / Production host: ![]() ![]() |
#7: Protein | Mass: 13317.060 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm7, SPCC285.12 / Production host: ![]() ![]() |
-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.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm3, SPBC9B6.05c / Production host: ![]() ![]() |
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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.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm4, SPBC30D10.06 / Production host: ![]() ![]() |
-RNA chain / Non-polymers , 2 types, 303 molecules H![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: RNA chain | Mass: 1815.077 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.54 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976177 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→98.8 Å / Num. obs: 75844 / % possible obs: 100 % / Redundancy: 31.4 % / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.81→1.88 Å / Num. unique obs: 4347 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.81→34.5 Å
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