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- PDB-1n87: Solution structure of the U-box of Prp19 -

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Basic information

Entry
Database: PDB / ID: 1n87
TitleSolution structure of the U-box of Prp19
ComponentsPre-mRNA splicing factor PRP19
KeywordsLIGASE/CELL CYCLE / Ubiquitin ligase / E3 ligase / U-box / LIGASE-CELL CYCLE COMPLEX
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / U2-type catalytic step 1 spliceosome / Prp19 complex / Dual incision in TC-NER / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...generation of catalytic spliceosome for first transesterification step / U2-type catalytic step 1 spliceosome / Prp19 complex / Dual incision in TC-NER / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type ...Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / Quinoprotein alcohol dehydrogenase-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Torsion angle dynamics, Molecular dynamics
AuthorsChazin, W.J. / Ohi, M.D. / Vander Kooi, C.W.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structural insights into the U-box, a domain associated with multi-ubiquitination
Authors: Ohi, M.D. / Vander Kooi, C.W. / Rosenberg, J.A. / Chazin, W.J. / Gould, K.L.
History
DepositionNov 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA splicing factor PRP19


Theoretical massNumber of molelcules
Total (without water)6,2461
Polymers6,2461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Pre-mRNA splicing factor PRP19


Mass: 6246.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Prp19 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32523

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY
1543D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Prp19(1-73); UL 20mM phosphate buffer pH 7.0; 20mM NaCl95% H2O/5% D2O
21mM Prp19(1-73); U-15N 20mM phosphate buffer pH 7.0; 20mM NaCl95% H2O/5% D2O
31mM Prp19(1-73); U-15N,13C 20mM phosphate buffer pH 7.0; 20mM NaCl95% H2O/5% D2O
41mM Prp19(1-73); U-15N,13C 20mM phosphate buffer pH 7.0; 20mM NaCl99% D2O
Sample conditionsIonic strength: 0.28 / pH: 7.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
XwinNMR2.6Brukercollection
XEASY1.3Bartelsdata analysis
Amber6Pearlmanrefinement
RefinementMethod: Torsion angle dynamics, Molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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