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- PDB-1zr7: Solution structure of the first WW domain of FBP11 -

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Basic information

Entry
Database: PDB / ID: 1zr7
TitleSolution structure of the first WW domain of FBP11
Componentshuntingtin-interacting protein HYPA/FBP11
KeywordsSIGNALING PROTEIN / beta sheet / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / nuclear matrix / mRNA splicing, via spliceosome / 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 / nuclear matrix / mRNA splicing, via spliceosome / cell migration / regulation of cell shape / nuclear speck / cell cycle / cell division / RNA binding / nucleoplasm / membrane
Similarity search - Function
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. ...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 / torsion angle dynamics
Model type detailsminimized average
AuthorsKato, Y. / Hino, Y. / Tanokura, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2006
Title: Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III
Authors: Kato, Y. / Hino, Y. / Nagata, K. / Tanokura, M.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)3,6131
Polymers3,6131
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)20 / 100target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide huntingtin-interacting protein HYPA/FBP11 / formin binding protein 11 (FBP11)/huntingtin yeast partner a (HYPA)


Mass: 3612.758 Da / Num. of mol.: 1 / Fragment: residues in database 150-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP11 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 3341990, UniProt: O75400*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.5mM FBP11 WW1 U-15N, 13C; 50mM phosphate buffer Na; 50mM NaCl, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0.175 / pH: 5.0 / Pressure: ambient / Temperature: 298 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
CYANA2Guntertstructure solution
CYANA2Guntertrefinement
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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