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Open data
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Basic information
Entry | Database: PDB / ID: 4emk | ||||||
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Title | Crystal structure of SpLsm5/6/7 | ||||||
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![]() | RNA BINDING PROTEIN / Sm fold / mRNA decay and pre-mRNA splicing / Lsm proteins | ||||||
Function / homology | ![]() mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / U2 snRNP ...mRNA decay by 5' to 3' exoribonuclease / Lsm2-8 complex / Lsm1-7-Pat1 complex / U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / U2 snRNP / tRNA processing / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / telomerase holoenzyme complex assembly / U5 snRNP / U2 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / nucleolus / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, S.M. / Wu, D.H. / Song, H.W. | ||||||
![]() | ![]() Title: Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe. Authors: Wu, D.H. / Jiang, S.M. / Bowler, M.W. / Song, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 39.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 454.7 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10807.282 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / Gene: lsm5, SPBC20F10.09 / Production host: ![]() ![]() |
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#2: Protein | Mass: 8439.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / Gene: lsm6, SPAC2F3.17c / Production host: ![]() ![]() |
#3: Protein | Mass: 12628.864 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / Gene: lsm7, SPCC285.12 / Production host: ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.28 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, pH 6.5, 0.1M MgCl2, 32% polyethylene glycol (PEG) 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→86.16 Å / Num. all: 19618 / Num. obs: 19618 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.62 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→54.053 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: 7
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