+Open data
-Basic information
Entry | Database: PDB / ID: 1qoi | ||||||
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Title | U4/U6 snRNP-specific cyclophilin SnuCyp-20 | ||||||
Components | SNUCYP-20 | ||||||
Keywords | ISOMERASE / SNUCYP-20 / CYCLOPHILIN / SNRNP / SPLICEOSOMAL | ||||||
Function / homology | Function and homology information U4/U6 snRNP / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex ...U4/U6 snRNP / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spliceosomal complex / mRNA splicing, via spliceosome / SARS-CoV-1 activates/modulates innate immune responses / protein folding / protein-containing complex assembly / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Reidt, U. / Reuter, K. / Achsel, T. / Ingelfinger, D. / Luehrmann, R. / Ficner, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Crystal Structure of the Human U4/U6 Small Nuclear Ribonucleoproteinparticle-Specificsnucyp-20, a Nuclear Cyclophilin Authors: Reidt, U. / Reuter, K. / Achsel, T. / Ingelfinger, D. / Luehrmann, R. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qoi.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qoi.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qoi ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qoi | HTTPS FTP |
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-Related structure data
Related structure data | 2cplS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19230.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA / Cellular location: NUCLEUS / Gene: SNUCYP-20 / Organelle: NUCLEUS / Plasmid: PGEX-4T-2 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43447 |
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#2: 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: 2.28 Å3/Da / Density % sol: 45.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 25% PEG6000, 200 MM MGCL2, 100 MM TRISHCL, PH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 12102 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.053 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 9.3 / Rsym value: 0.115 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 44280 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.115 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CPL Resolution: 2→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 8.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.191 |