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Open data
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Basic information
Entry | Database: PDB / ID: 6ppp | ||||||
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Title | Structure of S. pombe Lsm2-8 with processed U6 snRNA | ||||||
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![]() | RNA BINDING PROTEIN/RNA / ![]() ![]() | ||||||
Function / homology | ![]() mRNA decay by 5' to 3' exoribonuclease / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 481.1 KB | Display | ![]() |
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PDB format | ![]() | 376.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ppnC ![]() 6ppqC ![]() 6ppvC ![]() 4c92S ![]() 4emgS ![]() 4emhS ![]() 4emkS ![]() 4m7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-U6 snRNA-associated Sm-like protein ... , 5 types, 10 molecules BJEMFNGOHP
#2: Protein | Mass: 11003.798 Da / Num. of mol.: 2 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.: 2 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.: 2 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm7, SPCC285.12 / Production host: ![]() ![]() ![]() #8: Protein | Mass: 10572.005 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm8, SPCC1840.10 / Production host: ![]() ![]() ![]() |
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-Probable U6 snRNA-associated Sm-like protein ... , 2 types, 4 molecules CKDL
#3: Protein | Mass: 10824.278 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm3, SPBC9B6.05c / Production host: ![]() ![]() ![]() #4: Protein | Mass: 15007.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 972 / ATCC 24843 / Gene: lsm4, SPBC30D10.06 / Production host: ![]() ![]() ![]() |
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-RNA chain / Non-polymers , 2 types, 28 molecules AI![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: RNA chain | Mass: 1815.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion Details: 50 mM KCl 50 mM HEPES pH 7 Pentaerythritol propoxylate (5/4 PO/OH) |
-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: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.33→78 Å / Num. obs: 28712 / % possible obs: 43.7 % / Redundancy: 86.9 % / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.33→2.73 Å / Num. unique obs: 1433 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4EMG, 4EMH, 4EMK, 4C92, 4M7D Resolution: 2.33→51.7 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 2.33→51.7 Å
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