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- PDB-2kh9: Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA -

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Basic information

Entry
Database: PDB / ID: 2kh9
TitleSolution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA
Components
  • 5'-R(*AP*GP*AP*GP*AP*U)-3'
  • U4/U6 snRNA-associated-splicing factor PRP24
KeywordsSPLICING/RNA / Protein/RNA / RRM / snRNP / Splicing / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / SPLICING-RNA COMPLEX
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
RNA / U4/U6 snRNA-associated-splicing factor PRP24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMartin-Tumasz, S.A. / Butcher, S.E.
CitationJournal: Rna / Year: 2010
Title: Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24.
Authors: Martin-Tumasz, S. / Reiter, N.J. / Brow, D.A. / Butcher, S.E.
History
DepositionMar 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: 5'-R(*AP*GP*AP*GP*AP*U)-3'


Theoretical massNumber of molelcules
Total (without water)12,7812
Polymers12,7812
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 10841.389 Da / Num. of mol.: 1 / Fragment: UNP residues 115-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP24, YMR268C, YM8156.10C / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P49960
#2: RNA chain 5'-R(*AP*GP*AP*GP*AP*U)-3'


Mass: 1939.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-13C HSQC
1232D 1H-15N HSQC
1322D 1H-13C HSQC
1433D CBCA(CO)NH
1533D C(CO)NH
1633D HNCO
1733D HN(CA)CB
1833D HBHA(CO)NH
1933D (H)CCH-TOCSY
11033D 1H-15N NOESY
11123D 1H-13C NOESY
11222D 1H-1H NOESY
11312D 1H-1H NOESY
11432D 1H-15N HSQC-IPAP
11552D 1H-15N HSQC-IPAP
11633D J MODULATED CHSQC
11753D J MODULATED CHSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM Prp24-RRM2-1, 3 mM AGAGAU-2, 10 mM [U-2H] TRIS-3, 50 mM potassium chloride-4, 100% D2O100% D2O
2500 uM [U-99% 15N] Prp24-RRM2-5, 5 mM AGAGAU-6, 10 mM [U-2H] TRIS-7, 50 mM potassium chloride-8, 100% D2O100% D2O
3500 mM [U-99% 13C; U-99% 15N] Prp24-RRM2-9, 5 mM AGAGAU-10, 10 mM TRIS-11, 50 mM potassium chloride-12, 1 mM DTT-13, 90% H2O/10% D2O90% H2O/10% D2O
4500 uM [U-99% 13C; U-99% 15N] Prp24-RRM2-14, 5 mM AGAGAU-15, 10 mM TRIS-16, 50 mM potassium chloride-17, 1 mM DTT-18, 10 uM DSS-19, 90% H2O/10% D2O90% H2O/10% D2O
5300 uM [U-99% 13C; U-99% 15N] Prp24-RRM2-20, 3 mM AGAGAU-21, 10 mM TRIS-22, 50 mM potassium chloride-23, 1 mM DTT-24, 6.5 % DMPC/DHPC 3:1-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMPrp24-RRM2-11
3 mMAGAGAU-21
10 mMTRIS-3[U-2H]1
50 mMpotassium chloride-41
500 uMPrp24-RRM2-5[U-99% 15N]2
5 mMAGAGAU-62
10 mMTRIS-7[U-2H]2
50 mMpotassium chloride-82
500 mMPrp24-RRM2-9[U-99% 13C; U-99% 15N]3
5 mMAGAGAU-103
10 mMTRIS-113
50 mMpotassium chloride-123
1 mMDTT-133
500 uMPrp24-RRM2-14[U-99% 13C; U-99% 15N]4
5 mMAGAGAU-154
10 mMTRIS-164
50 mMpotassium chloride-174
1 mMDTT-184
10 uMDSS-194
300 uMPrp24-RRM2-20[U-99% 13C; U-99% 15N]5
3 mMAGAGAU-215
10 mMTRIS-225
50 mMpotassium chloride-235
1 mMDTT-245
6.5 %DMPC/DHPC 3:1-255
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA9003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ..., and Kollmrefinement
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
AtnosCandidHerrmann, T., Guentert, P., Wuethrich, K.structure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
HADDOCK2Dominguez, C., Boelens, R., Bonvin, A.M.M.J.refinement
HADDOCK2Dominguez, C., Boelens, R., Bonvin, A.M.M.J.structure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1466 / NOE intraresidue total count: 230 / NOE long range total count: 427 / NOE medium range total count: 353 / NOE sequential total count: 456 / Hydrogen bond constraints total count: 43 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 43 / Protein psi angle constraints total count: 43
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 7.5 ° / Maximum upper distance constraint violation: 0.38 Å / Torsion angle constraint violation method: HADDOCK Output
NMR ensemble rmsDistance rms dev: 0.015 Å / Distance rms dev error: 0.002 Å

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