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- PDB-1qoi: U4/U6 snRNP-specific cyclophilin SnuCyp-20 -

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Basic information

Entry
Database: PDB / ID: 1qoi
TitleU4/U6 snRNP-specific cyclophilin SnuCyp-20
ComponentsSNUCYP-20
KeywordsISOMERASE / SNUCYP-20 / CYCLOPHILIN / SNRNP / SPLICEOSOMAL
Function / homology
Function and homology information


U4/U6 snRNP / cyclosporin A binding / positive regulation of viral genome replication / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / mRNA Splicing - Major Pathway / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase ...U4/U6 snRNP / cyclosporin A binding / positive regulation of viral genome replication / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / mRNA Splicing - Major Pathway / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / 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 / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase H
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReidt, U. / Reuter, K. / Achsel, T. / Ingelfinger, D. / Luehrmann, R. / Ficner, R.
CitationJournal: 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
DepositionNov 9, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SNUCYP-20


Theoretical massNumber of molelcules
Total (without water)19,2301
Polymers19,2301
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.300, 59.900, 60.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SNUCYP-20 / USA-CYP


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.7 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2120 mM1dropNaCl
32 mMdithiothreitol1drop
420 mMHEPES1drop
525 %(w/v)PEG60001reservoir
6200 mM1reservoirMgCl2
7100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 15, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 12102 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.053
Reflection shellResolution: 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

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CPL

2cpl


Resolution: 2→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1251 10.3 %RANDOM
Rwork0.17 ---
obs0.17 12099 100 %-
Displacement parametersBiso mean: 8.4 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 0 181 1504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.79
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.221 149 11.2 %
Rwork0.191 1413 -
obs--100 %
Xplor fileSerial 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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor obs: 0.191

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