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- PDB-1mzw: Crystal structure of a U4/U6 snRNP complex between human spliceos... -

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Basic information

Entry
Database: PDB / ID: 1mzw
TitleCrystal structure of a U4/U6 snRNP complex between human spliceosomal cyclophilin H and a U4/U6-60K peptide
Components
  • U-snRNP-associated cyclophilin
  • U4/U6 snrnp 60kDa protein
KeywordsISOMERASE / cyclophilin / peptidyl-prolyl-cis/trans isomerase / spliceosome / snRNP / U4/U6-60K protein / WD protein
Function / homology
Function and homology information


spliceosomal snRNP complex / U4/U6 snRNP / RNA splicing, via transesterification reactions / U4 snRNA binding / U2-type precatalytic spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / U6 snRNA binding / ribonucleoprotein complex binding ...spliceosomal snRNP complex / U4/U6 snRNP / RNA splicing, via transesterification reactions / U4 snRNA binding / U2-type precatalytic spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / positive regulation of viral genome replication / U6 snRNA binding / ribonucleoprotein complex binding / Cajal body / RNA processing / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / RNA splicing / 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 / nucleus / cytosol / cytoplasm
Similarity search - Function
PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / 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. ...PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
U4/U6 small nuclear ribonucleoprotein Prp4 / Peptidyl-prolyl cis-trans isomerase H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReidt, U. / Wahl, M.C. / Horowitz, D.S. / Luehrmann, R. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide
Authors: Reidt, U. / Wahl, M.C. / Fasshauer, D. / Horowitz, D.S. / Luehrmann, R. / Ficner, R.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U-snRNP-associated cyclophilin
B: U4/U6 snrnp 60kDa protein


Theoretical massNumber of molelcules
Total (without water)22,7282
Polymers22,7282
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.369, 59.526, 47.040
Angle α, β, γ (deg.)90.00, 110.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein U-snRNP-associated cyclophilin / cyclophilin H


Mass: 19230.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43447
#2: Protein/peptide U4/U6 snrnp 60kDa protein / WD splicing factor Prp4 / hPrp4 / U4/U6 small nuclear ribonucleo protein Prp4


Mass: 3498.044 Da / Num. of mol.: 1 / Fragment: residues 107-137, internal domain / Source method: obtained synthetically / Details: peptide B106-B136 was chemically synthesized / References: UniProt: O43172
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 %(w/v)PEG80001reservoir
2200 mMmagnesium acetate1reservoir
30.1 MHEPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2001 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 55492 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.063
Reflection shellResolution: 2→2.1 Å / Rsym value: 0.236 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 13762 / Num. measured all: 55492 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 99 % / Rmerge(I) obs: 0.236

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOI

1qoi


Resolution: 2→15 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1344 -RANDOM
Rwork0.195 ---
all0.195 ---
obs0.195 13458 99.2 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 0 260 1825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.28
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.212

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