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- PDB-2l9w: Solution Structure of the C-terminal domain of Prp24 -

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Basic information

Entry
Database: PDB / ID: 2l9w
TitleSolution Structure of the C-terminal domain of Prp24
ComponentsU4/U6 snRNA-associated-splicing factor PRP24
KeywordsSPLICING / RNA BINDING PROTEIN / RRM / U6 snRNP
Function / homology
Function and homology information


U6 snRNP / snRNA binding / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding / nucleus
Similarity search - Function
Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
U4/U6 snRNA-associated-splicing factor PRP24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsLowest Average Pairwise RMSD, model 15
AuthorsMartin-Tumasz, S.A. / Butcher, S.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop.
Authors: Martin-Tumasz, S. / Richie, A.C. / Clos, L.J. / Brow, D.A. / Butcher, S.E.
History
DepositionFeb 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U4/U6 snRNA-associated-splicing factor PRP24


Theoretical massNumber of molelcules
Total (without water)13,8531
Polymers13,8531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest average pairwise rmsd

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Components

#1: Protein U4/U6 snRNA-associated-splicing factor PRP24 / U4/U6 snRNP protein


Mass: 13853.064 Da / Num. of mol.: 1 / Fragment: C-terminal residues 292-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP24, YM8156.10C, YMR268C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P49960

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The solution structure of the C-terminal domain of Prp24, containing an RRM with flanking alpha helices.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D 1H-15N NOESY
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1922D 1H-13C HSQC aliphatic
11022D 1H-13C HSQC aromatic
11142D 1H-1H NOESY
11223D (H)CCH-TOCSY
11323D 1H-13C NOESY aliphatic
11423D 1H-13C NOESY aromatic
11532D 1H-13C HSQC aliphatic
21612D-NHSQC-IPAP
21752D-NHSQC-IPAP
21813D-Jmodulated-CHSQC
21953D-Jmodulated-CHSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 0.9 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM [U-99% 2H] potassium phosphate pH 6, 45 mM [U-99% 2H] potassium chloride, 100% D2O100% D2O
3600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 1 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
4600 uM L4W, 18 mM [U-99% 2H] potassium phosphate pH 6, 45 mM [U-99% 2H] potassium chloride, 100% D2O100% D2O
5600 uM [U-99% 13C; U-99% 15N] L4W, 18 mM potassium phosphate pH 6, 45 mM potassium chloride, 0.9 mM DTT, 6.5 % DMPC/DHPC q=3, 0.67 mg/mL CTAB, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uML4W-1[U-99% 13C; U-99% 15N]1
18 mMpotassium phosphate pH 6-21
45 mMpotassium chloride-31
0.9 mMDTT-41
600 uML4W-5[U-99% 13C; U-99% 15N]2
18 mMpotassium phosphate pH 6-6[U-99% 2H]2
45 mMpotassium chloride-7[U-99% 2H]2
600 uML4W-8[U-99% 13C; U-99% 15N]3
18 mMpotassium phosphate pH 6-93
45 mMpotassium chloride-103
1 uMDSS-113
600 uML4W-124
18 mMpotassium phosphate pH 6-13[U-99% 2H]4
45 mMpotassium chloride-14[U-99% 2H]4
600 uML4W-15[U-99% 13C; U-99% 15N]5
18 mMpotassium phosphate pH 6-165
45 mMpotassium chloride-175
0.9 mMDTT-185
6.5 %DMPC/DHPC q=3-195
0.67 mg/mLCTAB-205
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16 ambient 298 K
26 ambient 304 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Bruker DMXBrukerDMX7502
Varian Uniform NMR SystemVarianUniform NMR System9003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
XwinNMRBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
HADDOCK2Alexandre Bonvinrefinement
HADDOCK2Alexandre Bonvindata analysis
UNIO8Torsten Herrmannstructure solution
NMR Structure ToolsLawrence J Closdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1379 / NOE intraresidue total count: 460 / NOE long range total count: 284 / NOE medium range total count: 272 / NOE sequential total count: 363 / Hydrogen bond constraints total count: 53
NMR representativeSelection criteria: lowest average pairwise rmsd
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.333 Å
NMR ensemble rmsDistance rms dev: 0.02 Å

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