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- PDB-8p25: Solution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box -

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Basic information

Entry
Database: PDB / ID: 8p25
TitleSolution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box
ComponentsSplicing factor U2AF 65 kDa subunit,Far upstream element-binding protein 1
KeywordsSPLICING / regulation / protein-protein interaction / RRM
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / single-stranded DNA binding / nuclear speck / mRNA binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / U2 snRNP auxilliary factor, large subunit, splicing factor / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. ...: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / U2 snRNP auxilliary factor, large subunit, splicing factor / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / K Homology domain / K homology RNA-binding domain / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Splicing factor U2AF 65 kDa subunit / Far upstream element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHipp, C. / Sattler, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1935 #273941853 Germany
German Research Foundation (DFG)and SFB 1035 #201302640 Germany
CitationJournal: Mol.Cell / Year: 2023
Title: FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns.
Authors: Ebersberger, S. / Hipp, C. / Mulorz, M.M. / Buchbender, A. / Hubrich, D. / Kang, H.S. / Martinez-Lumbreras, S. / Kristofori, P. / Sutandy, F.X.R. / Llacsahuanga Allcca, L. / Schonfeld, J. / ...Authors: Ebersberger, S. / Hipp, C. / Mulorz, M.M. / Buchbender, A. / Hubrich, D. / Kang, H.S. / Martinez-Lumbreras, S. / Kristofori, P. / Sutandy, F.X.R. / Llacsahuanga Allcca, L. / Schonfeld, J. / Bakisoglu, C. / Busch, A. / Hanel, H. / Tretow, K. / Welzel, M. / Di Liddo, A. / Mockel, M.M. / Zarnack, K. / Ebersberger, I. / Legewie, S. / Luck, K. / Sattler, M. / Konig, J.
History
DepositionMay 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 19, 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: Splicing factor U2AF 65 kDa subunit,Far upstream element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)16,2961
Polymers16,2961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit,Far upstream element-binding protein 1 / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit ...U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit / FBP / FUSE-binding protein 1 / DNA helicase V / hDH V


Mass: 16296.167 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker,Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker,Chimeric construct of U2AF2 ...Details: Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker,Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker,Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker,Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-Box linked by a 14-GS linker
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65, FUBP1 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26368, UniProt: Q96AE4

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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
121isotropic22D 1H-13C HSQC aromatic
1152isotropic2(HB)CB(CGCD)HD
1162isotropic2(HB)CB(CGCDCE)HE
132isotropic12D 1H-13C HSQC aliphatic
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D H(CCO)NH
191isotropic13D C(CO)NH
1141isotropic43D HNHA
1102isotropic43D (H)CCH-TOCSY
1132isotropic43D (H)CCH-TOCSY
1111isotropic33D 1H-15N NOESY
1122isotropic33D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution20.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 100% D2O15N13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMChimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box[U-100% 13C; U-100% 15N]1
0.6 mMChimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box[U-100% 13C; U-100% 15N]2
Sample conditionsDetails: 20mM sodium phosphate, 50mM sodium chloride, pH 6.5, 2mM DTT
Ionic strength: 50mM NaCl mM / Label: conditions_NMR / 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 III5004
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCE III HDBrukerAVANCE III HD9503

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee W., Tonelli M., Markley J. L.chemical shift assignment
NMRFAM-SPARKYLee W., Tonelli M., Markley J. L.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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