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- PDB-4uqt: RRM-peptide structure in RES complex -

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Basic information

Entry
Database: PDB / ID: 4uqt
TitleRRM-peptide structure in RES complex
Components
  • PRE-MRNA-SPLICING FACTOR CWC26
  • U2 SNRNP COMPONENT IST3
KeywordsTRANSLATION
Function / homology
Function and homology information


maintenance of RNA location / RES complex / generation of catalytic spliceosome for first transesterification step / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / mRNA export from nucleus / spliceosomal complex ...maintenance of RNA location / RES complex / generation of catalytic spliceosome for first transesterification step / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / spliceosomal complex assembly / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / nucleus / cytoplasm
Similarity search - Function
Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / 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
U2 snRNP component IST3 / Pre-mRNA-splicing factor CWC26
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsTripsianes, K. / Friberg, A. / Barrandon, C. / Seraphin, B. / Sattler, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Novel Protein-Protein Interaction in the Res (Retention and Splicing) Complex.
Authors: Tripsianes, K. / Friberg, A. / Barrandon, C. / Brooks, M. / Van Tilbeurgh, H. / Seraphin, B. / Sattler, M.
History
DepositionJun 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Atomic model / Database references / Other
Revision 1.2Oct 22, 2014Group: Database references
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_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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: U2 SNRNP COMPONENT IST3
B: PRE-MRNA-SPLICING FACTOR CWC26


Theoretical massNumber of molelcules
Total (without water)15,0712
Polymers15,0712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein U2 SNRNP COMPONENT IST3 / INCREASED SODIUM TOLERANCE PROTEIN 3 / U2 SNRNP PROTEIN SNU17 / SNU17P


Mass: 10538.707 Da / Num. of mol.: 1 / Fragment: RRM, RESIDUES 25-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS 24D / References: UniProt: P40565
#2: Protein/peptide PRE-MRNA-SPLICING FACTOR CWC26 / BUD SITE SELECTION PROTEIN 13 / COMPLEXED WITH CEF1 PROTEIN 26 / SYNTHETIC LETHAL WITH CLF1 PROTEIN 7 / BUD13P


Mass: 4532.087 Da / Num. of mol.: 1 / Fragment: TRP-CONTAINING LIGAND, RESIDUES 222-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS 24D / References: UniProt: P46947
Sequence detailsFIRST FOUR RESIDUES OF THE PROTEIN SEQUENCE (GAMG) ARE COMING FROM THE TAG.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED 3D NOESY
12113C- EDITED 3D NOESY (ALIPHATICS)
13113C-EDITED 3D NOESY (AROMATICS)
14113C- EDITED 3D NOESY (ALIPHATICSS) F1 15N/13C FILTERED
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON STOICHIOMETRIC COMPLEX SAMPLES WHERE ONLY SNU17P OR BUD13P WAS 13C, 15N-LABELED

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Sample preparation

DetailsContents: 93% WATER/7% D2O
Sample conditionsIonic strength: 25 mM / pH: 6.3 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON, WARRENrefinement
CcpNmr Analysis2.1structure solution
CYANAstructure solution
CNSstructure solution
TALOSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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