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- PDB-2dyf: Solution structure of the first WW domain of FBP11 / HYPA (FBP11 ... -

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Basic information

Entry
Database: PDB / ID: 2dyf
TitleSolution structure of the first WW domain of FBP11 / HYPA (FBP11 WW1) complexed with a PL (PPLP) motif peptide ligand
Components
  • Huntingtin-interacting protein HYPA/FBP11
  • PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1
KeywordsPROTEIN BINDING / WW DOMAIN / COMPLEX / FBP11 / HYPA / PL MOTIF / PPLP MOTIF / SOLUTION STRUCTURE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


myosin I tail binding / myosin I binding / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis ...myosin I tail binding / myosin I binding / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / nuclear matrix / mRNA splicing, via spliceosome / cell migration / regulation of cell shape / actin cytoskeleton organization / cell cycle / nuclear speck / cell division / nucleolus / RNA binding / nucleoplasm / membrane
Similarity search - Function
Mti1, SH3 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 ...Mti1, SH3 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 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Pre-mRNA-processing factor 40 homolog A / Myosin tail region-interacting protein MTI1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsKato, Y. / Miyakawa, T. / Kurita, J. / Tanokura, M.
CitationJournal: To be Published
Title: Complex structure of fbp11 ww1 and a pl ligand reveals the mechanism of proline-rich ligand recognition by group-II/III ww domains
Authors: Kato, Y. / Miyakawa, T. / Kurita, J. / Tanokura, M.
History
DepositionSep 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / 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_exptl_sample_conditions.pressure_units / _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: Huntingtin-interacting protein HYPA/FBP11
B: PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)4,5092
Polymers4,5092
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)20 / 100target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Huntingtin-interacting protein HYPA/FBP11 / Pre-mRNA-processing factor 40 homolog A / Formin-binding protein 3 / Huntingtin yeast partner A / ...Pre-mRNA-processing factor 40 homolog A / Formin-binding protein 3 / Huntingtin yeast partner A / Fas ligand-associated factor 1 / NY-REN-6 antigen


Mass: 3612.758 Da / Num. of mol.: 1 / Fragment: THE FIRST WW DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75400
#2: Protein/peptide PL (PPLP) motif peptide from Myosin tail region-interacting protein MTI1 / Protein BBC1


Mass: 896.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47068

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
121HNHA
1313D 15N-SEPARATED NOESY
NMR detailsText: This structure was determined using standard 3D Heteronuclear techniques and 13C half filtered noesy-hsqc.

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Sample preparation

DetailsContents: 1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF ...Contents: 1.5MM FBP11 WW1 U-15N, 13C 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.5MM FBP11 WW1 U- 15N, 13C; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O; 1.6MM FBP11 WW1 NATURAL ABUNDANCE; 4.4MM PL MOTIF PEPTIDE U-15N, 13C; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 100% D2O; 1.5MM FBP11 WW1 U-15N; 5.3MM NATURAL ABUNDANCE PL MOTIF PEPTIDE; 50MM PHOSPHATE BUFFER NA; 50MM NACL; 90% H2O, 10% D2O
Sample conditionsIonic strength: 0.3 / pH: 5.0 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2HERRMANN, GUENTERT, WUETHRICHrefinement
CYANA2structure solution
NMRPipestructure solution
Sparky3structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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