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- PDB-2kfd: Prp40 FF4 domain -

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Basic information

Entry
Database: PDB / ID: 2kfd
TitlePrp40 FF4 domain
ComponentsPre-mRNA-processing protein PRP40
KeywordsNUCLEAR PROTEIN / FF domain / Prp40 / Saccharomyces cerevisiae / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Ribonucleoprotein
Function / homology
Function and homology information


commitment complex / U1 snRNP / U2-type prespliceosome / mRNA 5'-splice site recognition / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / nucleus
Similarity search - Function
FF domain / Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...FF domain / Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-processing protein PRP40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsBonet, R. / Ruiz, L. / Morales, B. / Macias, M.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of the fourth FF domain of yeast Prp40 splicing factor.
Authors: Bonet, R. / Ruiz, L. / Morales, B. / Macias, M.J.
History
DepositionFeb 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing protein PRP40


Theoretical massNumber of molelcules
Total (without water)8,2161
Polymers8,2161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pre-mRNA-processing protein PRP40


Mass: 8216.300 Da / Num. of mol.: 1 / Fragment: UNP residues 488-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP40, YKL012W, YKL165 / Production host: Escherichia coli (E. coli) / References: UniProt: P33203

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D H(CCO)NH
1623D (H)CCH-TOCSY
1723D 1H-15N NOESY
1823D 1H-13C NOESY
1922D 1H-15N HSQC
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM yeast Prp40 FF4 domain-1, 20 mM sodium phosphate-2, 130 mM sodium chloride-3, 0.5 mM sodium azide-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 15N] yeast Prp40 FF4 domain-5, 0.5 mM [U-100% 13C] yeast Prp40 FF4 domain-6, 20 mM sodium phosphate-7, 130 mM sodium chloride-8, 0.5 mM sodium azide-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMyeast Prp40 FF4 domain-11
20 mMsodium phosphate-21
130 mMsodium chloride-31
0.5 mMsodium azide-41
0.5 mMyeast Prp40 FF4 domain-5[U-100% 15N]2
0.5 mMyeast Prp40 FF4 domain-6[U-100% 13C]2
20 mMsodium phosphate-72
130 mMsodium chloride-82
0.5 mMsodium azide-92
Sample conditionsIonic strength: 150 / pH: 5.8 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2Linge, O'Donoghue and Nilgesstructure solution
ARIA2Linge, O'Donoghue and Nilgesrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 15

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