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- PDB-7aaf: Structural evolution of the tissue-specific U2AF2 paralog and alt... -

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Basic information

Entry
Database: PDB / ID: 7aaf
TitleStructural evolution of the tissue-specific U2AF2 paralog and alternative splicing factor LS2
ComponentsU2 snRNP auxiliary factor large subunit
KeywordsRNA BINDING PROTEIN / alternative splicing / structural biology / G quadruplex / U2AF / LS2 / RRM RNA binding domain / RNA-protein interactions
Function / homology
Function and homology information


: / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / negative regulation of RNA splicing / commitment complex / U2-type prespliceosome / RNA splicing / mRNA processing / nuclear speck ...: / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / negative regulation of RNA splicing / commitment complex / U2-type prespliceosome / RNA splicing / mRNA processing / nuclear speck / mRNA binding / RNA binding
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Similarity search - Domain/homology
U2 snRNP auxiliary factor large subunit
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsKawale, A.A. / Kang, H.S. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structural evolution of the tissue-specific U2AF2 paralog and alternative splicing factor LS2
Authors: Kawale, A.A. / Kang, H.S. / Sattler, M.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U2 snRNP auxiliary factor large subunit


Theoretical massNumber of molelcules
Total (without water)8,9071
Polymers8,9071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein U2 snRNP auxiliary factor large subunit


Mass: 8907.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: LS2, cg3162, Dmel\CG3162, CG3162, Dmel_CG3162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W1T4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D HNCA
181isotropic33D 1H-15N NOESY
161isotropic23D 1H-13C NOESY aliphatic
191isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM 13C 15N LS2 RRM2, 0.02 mM 13C 15N potassium phosphate pH 6.5, 0.05 mM 13C 15N sodium chloride, 0.002 mM 13C 15N DTT, 90% H2O/10% D2O
Label: 13C,15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLS2 RRM213C 15N1
0.02 mMpotassium phosphate pH 6.513C 15N1
0.05 mMsodium chloride13C 15N1
0.002 mMDTT13C 15N1
Sample conditionsIonic strength: 0.07 mM / Label: LS2 RRM2 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE 750BrukerAVANCE 7507501
Bruker AVANCE 800BrukerAVANCE 8008002
Bruker AVANCE 900BrukerAVANCE 9009003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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