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- PDB-2jxw: Solution Structure of the Tandem WW Domains of FBP21 -

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Basic information

Entry
Database: PDB / ID: 2jxw
TitleSolution Structure of the Tandem WW Domains of FBP21
ComponentsWW domain-binding protein 4
KeywordsFORMIN BINDING PROTEIN / WW domain containing protein / WW domain / FBP21 / WBP4 / Metal-binding / mRNA processing / mRNA splicing / Nucleus / Polymorphism / Spliceosome / Zinc / Zinc-finger
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / precatalytic spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / nuclear speck / RNA binding / zinc ion binding ...mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / precatalytic spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / nuclear speck / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
WW domain-binding protein 4 / U1-C, C2H2-type zinc finger / U1 zinc finger / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / WW domain ...WW domain-binding protein 4 / U1-C, C2H2-type zinc finger / U1 zinc finger / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Zinc finger C2H2 superfamily / Single Sheet / Mainly Beta
Similarity search - Domain/homology
WW domain-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, X. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21)
Authors: Huang, X. / Beullens, M. / Zhang, J. / Zhou, Y. / Nicolaescu, E. / Lesage, B. / Hu, Q. / Wu, J. / Bollen, M. / Shi, Y.
History
DepositionNov 30, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WW domain-binding protein 4


Theoretical massNumber of molelcules
Total (without water)8,6881
Polymers8,6881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein WW domain-binding protein 4 / WBP-4 / WW domain-containing-binding protein 4 / Formin-binding protein 21 / FBP21


Mass: 8688.309 Da / Num. of mol.: 1 / Fragment: WW Domian
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WBP4, FBP21, FNBP21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D 1H-15N NOESY
1513D 1H-13C NOESY
2612D 1H-1H TOCSY
2712D 1H-1H NOESY
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D HBHA(CO)NH
11113D H(CCO)NH
11213D HNCO
11313D HN(CO)CA
11413D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM [U-99% 13C; U-99% 15N] FBP21; 90% H2O/10% D2O90% H2O/10% D2O
20.5mM [U-99% 15N] FBP21; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity[U-99% 13C; U-99% 15N]1
0.5 mMentity[U-99% 15N]2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 1 atm293 K
26.5 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures cannot be superimposed as a entire molecule due to the flexible linker. It's only can be superimposed in the WW domain region respectively. Taking each domain individually(6- ...Details: The structures cannot be superimposed as a entire molecule due to the flexible linker. It's only can be superimposed in the WW domain region respectively. Taking each domain individually(6-32AA and 47-73AA), the r.m.s.d. values close is to 0.4 for backbone.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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