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- PDB-2yh0: Solution structure of the closed conformation of human U2AF65 tan... -

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Basic information

Entry
Database: PDB / ID: 2yh0
TitleSolution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains
ComponentsSPLICING FACTOR U2AF 65 KDA SUBUNIT
KeywordsTRANSCRIPTION / PRE-MRNA SPLICING / RNA BINDING PROTEIN / MRNA PROCESSING
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 / 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 / MODIFIED ARIA
AuthorsMackereth, C.D. / Madl, T. / Simon, B. / Zanier, K. / Gasch, A. / Sattler, M.
CitationJournal: Nature / Year: 2011
Title: Multi-Domain Conformational Selection Underlies Pre-Mrna Splicing Regulation by U2Af
Authors: Mackereth, C.D. / Madl, T. / Bonnal, S. / Simon, B. / Zanier, K. / Gasch, A. / Rybin, V. / Valcarcel, J. / Sattler, M.
History
DepositionApr 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Atomic model / Database references / Other
Revision 1.2Sep 25, 2019Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)21,5111
Polymers21,5111
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 / 500LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein SPLICING FACTOR U2AF 65 KDA SUBUNIT / U2 AUXILIARY FACTOR 65 KDA SUBUNIT / HUMAN U2AF65 / U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT / HU2AF(65)


Mass: 21510.525 Da / Num. of mol.: 1
Fragment: TANDEM RRM1 AND RRM2 DOMAINS JOINED BY NATIVE LINKER, RESIDUES 148-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P26368

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H
12115N HSQC (PRE)

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 70 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 295.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: MODIFIED ARIA / Software ordinal: 1
Details: FINAL WATER REFINEMENT. THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL. FIRST WITH REFINEMENT OF INDIVIDUAL STRUCTURED DOMAINS FOR RRM1 AND RRM2 OF U2AF65. THE INITIAL COORDINATES ...Details: FINAL WATER REFINEMENT. THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL. FIRST WITH REFINEMENT OF INDIVIDUAL STRUCTURED DOMAINS FOR RRM1 AND RRM2 OF U2AF65. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ID 2G4B BY SICKMIER ET AL. 2006. MOL. CELL 23, 49- 59. SECOND STEP IS ADDITION AND RANDOMIZATION OF FLEXIBLE AND LINKER RESIDUES. THE THIRD STEP IS MODEL CALCULATION USING RDC ORIENTATION, PRE-BASED DISTANCE, TALOS DIHEDRAL AND HYDROGEN BOND RESTRAINTS WITH THE RRM1 AND RRM2 DOMAINS RESTRAINED TO THEIR INITIAL STARTING STRUCTURES. STRUCTURE CALCULATION INCLUDED DISTANCE RESTRAINTS BASED ON PARAMAGNETIC RELAXATION ENHANCEMENT DATA FROM SEVEN INDEPENDENT CYSTEINE MUTANTS (N155C, A164C, A171C, T209C, D273C, A287C AND A318C) COVALENTLY MODIFIED BY 3-(2- IODOACETAMIDO)-2,2,5,5, TETRAMETHYL-1- PYRROLIDINYLOXY RADICAL (IODOACETAMIDO-PROXYL).
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 500 / Conformers submitted total number: 10

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