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- PDB-1o6w: Solution Structure of the Prp40 WW Domain Pair of the Yeast Splic... -

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Basic information

Entry
Database: PDB / ID: 1o6w
TitleSolution Structure of the Prp40 WW Domain Pair of the Yeast Splicing Factor Prp40
ComponentsPRE-MRNA PROCESSING PROTEIN PRP40Post-transcriptional modification
KeywordsNUCLEAR PROTEIN / WW DOMAIN PAIR / MRNA PROCESSING / PRP40 / MRNA SPLICING / 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
Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / WW domain / WW/rsp5/WWP domain signature. ...Pre-mRNA-processing factor Prp40 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Pre-mRNA-processing protein PRP40
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WIT TORSION ANGLE DYNAMICS AS IMPLEMENTED IN ARIA1.0
AuthorsWiesner, S. / Stier, G. / Sattler, M. / Macias, M.J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution Structure and Ligand Recognition of the Ww Domain Pair of the Yeast Splicing Factor Prp40
Authors: Wiesner, S. / Stier, G. / Sattler, M. / Macias, M.J.
History
DepositionOct 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)8,8971
Polymers8,8971
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)7 / 20STRUCTURES WITH ACCEPTABLE COVALEN GEOMETRY, STRUCTURES WITH FAVORABL NON-BOND ENERGY
RepresentativeModel #1

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Components

#1: Protein PRE-MRNA PROCESSING PROTEIN PRP40 / Post-transcriptional modification / PRP40


Mass: 8897.083 Da / Num. of mol.: 1 / Fragment: WW DOMAIN PAIR, RESIDUES 1-75
Source method: isolated from a genetically manipulated source
Details: WW DOMAIN PAIR OF SC. PRE-MRNA PROCESSING PROTEIN (PRP) 40
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Description: N-TERMINAL HIS6-TAG AND TEV CLEAVAGE SITE / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33203
Compound detailsREQUIRED FOR THE FIRST STEP OF PRE-MRNA SPLICING. THIS PROTEIN IS ASSOCIATED WITH SNRNP U1.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-NOESY
12115N-NOESY
131S3CT
141HNCG
151HNHA-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C,15N-LABELED PRP40 1-75. RESIDUAL DIPOLAR COUPLINGS WERE MEASURED TO INCREASE THE CONVERGENCE OF THE SET OF STUCTURES CALCULATED.

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Sample preparation

Details
Solution-IDContents
11.5 MM 15N- OR 13C,15N
220MM PHOSPHATE BUFFER PH 6.3
330MM NACL
40.03% (W/V) NAN3
Sample conditionsIonic strength: 20MM NA PHOSPHATE, 30MM NACL / pH: 6.3 / Pressure: 1 atm / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIANILGES, M.refinement
XEASYstructure solution
NMRViewstructure solution
PIPP/ CAPPCAPPstructure solution
ARIAstructure solution
CNSstructure solution
RefinementMethod: AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WIT TORSION ANGLE DYNAMICS AS IMPLEMENTED IN ARIA1.0
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALEN GEOMETRY, STRUCTURES WITH FAVORABL NON-BOND ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 7

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