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- PDB-3siv: Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form -
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Open data
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Basic information
Entry | Database: PDB / ID: 3siv | ||||||
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Title | Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form | ||||||
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![]() | SPLICING/RNA / Major and minor spliceosome / pre-mRNA splicing / RNA-protein complex / U4 snRNP and U4atac snRNP / RNA-binding protein / U4 snRNA / nucleus / SPLICING-RNA complex | ||||||
Function / homology | ![]() ribonucleoprotein complex localization / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / snRNP binding / U4 snRNA binding / box C/D methylation guide snoRNP complex / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome ...ribonucleoprotein complex localization / U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / snRNP binding / U4 snRNA binding / box C/D methylation guide snoRNP complex / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / U2-type spliceosomal complex / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / precatalytic spliceosome / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / Cajal body / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / ATPase binding / nuclear speck / nucleolus / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, S. / Ghalei, H. / Luhrmann, R. / Wahl, M.C. | ||||||
![]() | ![]() Title: Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31. Authors: Liu, S. / Ghalei, H. / Luhrmann, R. / Wahl, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360.1 KB | Display | ![]() |
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PDB format | ![]() | 289.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3siuC ![]() 2ozbS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THE PREDICTED HEXAMERIC COMPLEXES RESEMBLE DUPLICATED TRIMERIC COMPLEXES AS IN PDB ENTRY 3SIU. THE TRIMERIC COMPLEXES REPRESENT THE BIOLOGICALLY RELEVANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 14335.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 28268.225 Da / Num. of mol.: 4 / Fragment: UNP residues 85-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: RNA chain | Mass: 10344.204 Da / Num. of mol.: 4 / Fragment: GB bases 28-55 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.75 Å3/Da / Density % sol: 74.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.1 M sodium cacodylate, pH 6.4, 20% v/v PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 393K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9841 Å / Relative weight: 1 |
Reflection | Resolution: 3.304→30 Å / Num. all: 59914 / Num. obs: 59255 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 118.9 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4586 / Rsym value: 0.412 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 2OZB Resolution: 3.304→29.923 Å / SU ML: 0.42 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 26.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.754 Å2 / ksol: 0.274 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 138.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3.304→29.923 Å
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Refine LS restraints |
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LS refinement shell |
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