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- PDB-8pxx: Structure of the WW domain tandem of PRPF40A in complex with SF1 -

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Basic information

Entry
Database: PDB / ID: 8pxx
TitleStructure of the WW domain tandem of PRPF40A in complex with SF1
Components
  • Pre-mRNA-processing factor 40 homolog A
  • Splicing factor 1
KeywordsSPLICING / WW domain tandem / Proline-rich peptide / Alternative Splicing Regulation / E complex
Function / homology
Function and homology information


nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / spliceosomal complex assembly ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / U1 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / cytoskeleton organization / mRNA Splicing - Major Pathway / regulation of cytokinesis / negative regulation of smooth muscle cell proliferation / spliceosomal complex / nuclear matrix / mRNA splicing, via spliceosome / transcription corepressor activity / cell migration / regulation of cell shape / nuclear body / ribosome / nuclear speck / cell cycle / cell division / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / Pre-mRNA-processing factor Prp40 / KH domain-containing BBP-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / Pre-mRNA-processing factor Prp40 / KH domain-containing BBP-like / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Pre-mRNA-processing factor 40 homolog A / Splicing factor 1
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

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing factor 40 homolog A
B: Splicing factor 1


Theoretical massNumber of molelcules
Total (without water)13,8652
Polymers13,8652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable, gel filtration, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
#2: Protein/peptide Splicing factor 1 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene ...Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162


Mass: 2414.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
123isotropic32D 1H-15N HSQC
131isotropic33D HNCA
141isotropic33D HN(CA)CB
153isotropic33D HN(CA)CB
1123isotropic33D H(CCO)NH
1112isotropic12D 1H-13C HSQC aliphatic
1102isotropic12D 1H-13C HSQC aromatic
194isotropic22D 1H-13C HSQC aliphatic
182isotropic13D (H)CCH-TOCSY
174isotropic23D (H)CCH-TOCSY
161isotropic23D 1H-15N NOESY
1172isotropic23D 1H-13C NOESY
1164isotropic23D 1H-13C NOESY
1152isotropic13D 1H-13C filtered NOESY
1144isotropic23D 1H-13C filtered NOESY
1135isotropic32D DSSE-HSCQ
1186anisotropic32D DSSE-HSCQ

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 90% H2O/10% D2OWWlabelled_H2O90% H2O/10% D2O
solution2590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 100% D2OWWlabelled_D2O100% D2O
solution3900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 90% H2O/10% D2OSF1labelled_H2O90% H2O/10% D2O
solution4900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 100% D2OSF1labelled_D2O100% D2O
solution5150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 90% H2O/10% D2OIsotrop_RDC90% H2O/10% D2O
filamentous virus6150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 10 mg/mL Pf1 phage, 90% H2O/10% D2OAnisotrop_RDC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
590 uMPRPF40A[U-100% 13C; U-100% 15N]1
590 uMSF1natural abundance1
590 uMPRPF40A[U-100% 13C; U-100% 15N]2
590 uMSF1natural abundance2
900 uMSF1[U-100% 13C; U-100% 15N]3
900 uMPRPF40Anatural abundance3
900 uMSF1[U-100% 13C; U-100% 15N]4
900 uMPRPF40Anatural abundance4
150 uMPRPF40A[U-100% 15N]5
150 uMSF1natural abundance5
150 uMPRPF40A[U-100% 15N]6
150 uMSF1natural abundance6
10 mg/mLPf1 phagenatural abundance6
Sample conditionsIonic strength: 133 mM / Label: NMR-buffer / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III6003

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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
PALESMarkus Zweckstetterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 3
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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