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- PDB-1ywi: Structure of the FBP11WW1 domain complexed to the peptide APPTPPPLPP -

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Basic information

Entry
Database: PDB / ID: 1ywi
TitleStructure of the FBP11WW1 domain complexed to the peptide APPTPPPLPP
Components
  • Formin
  • Formin-binding protein 3
KeywordsSTRUCTURAL PROTEIN / WW domain / Class II / Proline-rich peptides / protein-protein interactions
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / mRNA splicing, via spliceosome / nuclear matrix / cell migration / regulation of cell shape ...mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / mRNA splicing, via spliceosome / nuclear matrix / cell migration / regulation of cell shape / nuclear speck / cell division / RNA binding / nucleoplasm / membrane
Similarity search - Function
PRPF40A-like, 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 ...PRPF40A-like, 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
Similarity search - Domain/homology
Pre-mRNA-processing factor 40 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Automated assignment of NOEs, simulated anneling with torsion angle dinamics
AuthorsPires, J.R. / Parthier, C. / Aido-Machado, R. / Wiedemann, U. / Otte, L. / Boehm, G. / Rudolph, R. / Oschkinat, H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural basis for APPTPPPLPP peptide recognition by the FBP11WW1 domain.
Authors: Pires, J.R. / Parthier, C. / Aido-Machado, R. / Wiedemann, U. / Otte, L. / Bohm, G. / Rudolph, R. / Oschkinat, H.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 29, 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: Formin-binding protein 3
B: Formin


Theoretical massNumber of molelcules
Total (without water)5,7302
Polymers5,7302
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)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Formin-binding protein 3 / Formin binding protein 11


Mass: 4747.092 Da / Num. of mol.: 1 / Fragment: WW1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O75400
#2: Protein/peptide Formin


Mass: 983.158 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: automated solid phase synthesis on chlortrityl resin using FMOC strategy

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Triple-resonance
1223D 13C-separated NOESY
1333D 15N-separated NOESY
1442D NOESY
1542D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8mM [U-15N,13C] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA90% H2O/10% D2O
21.8mM [U-15N,13C] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA100% D2O
31.8mM [U-15N] FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA90% H2O/10% D2O
41.8mM FBP11WW1, 3.6mM APPTPPPLPP, 10mM phosphate buffer, 100mM Nacl, 0.1mM DTT, 0.1mM EDTA90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1refinement
XwinNMR3.2Bruker AGcollection
XwinNMR3.2Bruker AGprocessing
Sparky3.1Goddard, T.D., Keneller, D.G., University of California San Franciscodata analysis
RefinementMethod: Automated assignment of NOEs, simulated anneling with torsion angle dinamics
Software ordinal: 1
Details: The structure was also refined with ARIA ver.1.2, authors: Linge, J.P., O'Dongue, S.I., Nilges, M.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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