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- PDB-2m09: Structure, phosphorylation and U2AF65 binding of the Nterminal Do... -

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Basic information

Entry
Database: PDB / ID: 2m09
TitleStructure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition
ComponentsSplicing factor 1
KeywordsTRANSCRIPTION / spliceosome assembly / SF1 / UHM / ULM / RRM
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 / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA splicing, via spliceosome / transcription corepressor activity / nuclear body / ribosome / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMadl, T. / Sattler, M. / Zhang, Y. / Bagdiul, I. / Kern, T. / Kang, H. / Zou, P. / Maeusbacher, N. / Sieber, S.A. / Kraemer, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition.
Authors: Zhang, Y. / Madl, T. / Bagdiul, I. / Kern, T. / Kang, H.S. / Zou, P. / Mausbacher, N. / Sieber, S.A. / Kramer, A. / Sattler, M.
History
DepositionOct 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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: Splicing factor 1


Theoretical massNumber of molelcules
Total (without water)13,8221
Polymers13,8221
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 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: 13821.770 Da / Num. of mol.: 1 / Fragment: UNP residues 27-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCA
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 100-600 uM [U-15N] protein, 100-600 uM [U-13C; U-15N] entity, 100-600 uM [U-13C; U-15N; U-2H] entity, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMprotein-1[U-15N]100-6001
uMprotein-2[U-13C; U-15N]100-6001
uMprotein-3[U-13C; U-15N; U-2H]100-6001
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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