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- PDB-2b7e: First FF domain of Prp40 Yeast Protein -

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Basic information

Entry
Database: PDB / ID: 2b7e
TitleFirst FF domain of Prp40 Yeast Protein
ComponentsPre-mRNA processing protein PRP40Post-transcriptional modification
KeywordsSTRUCTURAL PROTEIN
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 / torsion angle dynamics
AuthorsGasch, A. / Wiesner, S. / Martin-Malpartida, P. / Ramirez-Espain, X. / Ruiz, L. / Macias, M.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
Authors: Gasch, A. / Wiesner, S. / Martin-Malpartida, P. / Ramirez-Espain, X. / Ruiz, L. / Macias, M.J.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 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: Pre-mRNA processing protein PRP40


Theoretical massNumber of molelcules
Total (without water)7,1591
Polymers7,1591
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)12 / 20structures with the least restraint violations
Representative

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Components

#1: Protein Pre-mRNA processing protein PRP40 / Post-transcriptional modification


Mass: 7159.096 Da / Num. of mol.: 1 / Fragment: FF1 domain (residues 134-189)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP40 / 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 NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Prp40, 50mM phosphate buffer Na, 100mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
2Prp40 U-15N, 50mM phosphate buffer Na, 100 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
3Prp40 U-15N U-13C, 50mM phosphate buffer Na, 100 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12.2 5.5 1 atm285 K
22.2 5.5 1 atm280 K

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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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Brukercollection
NMRPipe3.6Delaglio, F.processing
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 12

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