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- PDB-6tr0: Solution structure of U2AF2 RRM1,2 -

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Basic information

Entry
Database: PDB / ID: 6tr0
TitleSolution structure of U2AF2 RRM1,2
ComponentsSplicing factor U2AF 65 kDa subunit
KeywordsSPLICING / 3'-splice site / polypyrimidine tract / splicing regulation
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 / nuclear speck / enzyme binding / RNA binding / nucleoplasm / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKang, H.-S. / Sattler, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2.
Authors: Kang, H.S. / Sanchez-Rico, C. / Ebersberger, S. / Sutandy, F.X.R. / Busch, A. / Welte, T. / Stehle, R. / Hipp, C. / Schulz, L. / Buchbender, A. / Zarnack, K. / Konig, J. / Sattler, M.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 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


Theoretical massNumber of molelcules
Total (without water)22,3421
Polymers22,3421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 22342.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Production host: Escherichia coli (E. coli) / References: UniProt: P26368

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic23D 1H-13C NOESY
131isotropic13D (H)CCH-TOCSY
141isotropic13D (H)CCH-COSY
151isotropic12D 1H-13C HSQC aromatic
171isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
181isotropic13D HNCO
191isotropic13D HN(CA)CO
1101isotropic12D 1H-15N HSQC
1111isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution / Contents: 0.5 mM [U-13C; U-15N] U2AF2, 90% H2O/10% D2O / Label: U2AF2 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: U2AF2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / 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 III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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