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- PDB-2m52: NMR Structure of the third RNA Recognition Motif (RRM) of U2 smal... -

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Basic information

Entry
Database: PDB / ID: 2m52
TitleNMR Structure of the third RNA Recognition Motif (RRM) of U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2
ComponentsSplicing factor U2AF 65 kDa subunit
KeywordsPROTEIN BINDING / RNA BINDING PROTEIN / RNA Recognition Motif / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / mRNA Splicing - Major Pathway / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / C2H2 zinc finger domain binding ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / mRNA Splicing - Major Pathway / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / C2H2 zinc finger domain binding / commitment complex / U2-type prespliceosome / molecular function inhibitor activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / positive regulation of RNA splicing / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR Structure of the third RNA Recognition Motif (RRM) of U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionFeb 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Structure summary
Revision 1.2Apr 10, 2013Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
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: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
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)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / U2 snRNP auxiliary factor large subunit


Mass: 12033.667 Da / Num. of mol.: 1 / Fragment: UNP residues 371-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: U2af2, U2af65 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26369

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1214D-HACANH-APSY
1315D-CBCA(CO)NH-APSY
1415D-(HA)CA(CO)NH-APSY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM sodium azide, 8 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
5 mMsodium azide-41
8 mMDTT-51
Sample conditionsIonic strength: 0.1298 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAG ntert P.structure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
j-UNIOHerrmann, Guntert and Wuthrichchemical shift assignment
j-UNIOHerrmann, Guntert and Wuthrichpeak picking
j-UNIOHerrmann, Guntert and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1920 / NOE intraresidue total count: 495 / NOE long range total count: 554 / NOE medium range total count: 340 / NOE sequential total count: 531
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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