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- PDB-8pxw: Structure of the WW domain tandem of PRPF40A -

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Basic information

Entry
Database: PDB / ID: 8pxw
TitleStructure of the WW domain tandem of PRPF40A
ComponentsPre-mRNA-processing factor 40 homolog A
KeywordsSPLICING / Dynamic WW domain tandem / Proline binding domain / Alternative Splicing Regulation / E complex
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 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 / simulated annealing
AuthorsMartinez-Lumbreras, S. / Sattler, M.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission792692European Union
German Research Foundation (DFG)SFB1035 - 201302640 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs.
Authors: Martinez-Lumbreras, S. / Trager, L.K. / Mulorz, M.M. / Payr, M. / Dikaya, V. / Hipp, C. / Konig, J. / Sattler, M.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-processing factor 40 homolog A


Theoretical massNumber of molelcules
Total (without water)11,4511
Polymers11,4511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, not applicable, NMR relaxation study, gel filtration
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 Pre-mRNA-processing factor 40 homolog A / Fas ligand-associated factor 1 / Formin-binding protein 11 / Formin-binding protein 3 / Huntingtin ...Fas ligand-associated factor 1 / Formin-binding protein 11 / Formin-binding protein 3 / Huntingtin yeast partner A / Huntingtin-interacting protein 10 / HIP-10 / Huntingtin-interacting protein A / Renal carcinoma antigen NY-REN-6


Mass: 11450.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF40A, FBP11, FLAF1, FNBP3, HIP10, HYPA, HSPC225 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75400

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D H(CCO)NH
171isotropic13D 1H-15N NOESY
182isotropic22D 1H-13C HSQC aliphatic
192isotropic22D 1H-13C HSQC aromatic
1102isotropic22D (HB)CB(CGCD)HD
1112isotropic22D (HB)CB(CGCDCE)HE
1122isotropic23D (H)CCH-TOCSY
1132isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1390 uM [U-100% 13C; U-100% 15N] PRPF40A, 90% H2O/10% D2OWW12_H2O90% H2O/10% D2O
solution2390 uM [U-100% 13C; U-100% 15N] PRPF40A, 100% D2OWW12_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
390 uMPRPF40A[U-100% 13C; U-100% 15N]1
390 uMPRPF40A[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 133 mM / Label: NMR-buffer / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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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