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- PDB-2adb: Solution structure of Polypyrimidine Tract Binding protein RBD2 c... -

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Basic information

Entry
Database: PDB / ID: 2adb
TitleSolution structure of Polypyrimidine Tract Binding protein RBD2 complexed with CUCUCU RNA
Components
  • 5'-R(*CP*UP*CP*UP*CP*U)-3'
  • Polypyrimidine tract-binding protein 1
KeywordsRNA BINDING PROTEIN/RNA / RBD / RRM / Protein-RNA Complex / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / : / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / 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
RNA / Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsOberstrass, F.C. / Auweter, S.D. / Erat, M. / Hargous, Y. / Henning, A. / Wenter, P. / Reymond, L. / Pitsch, S. / Black, D.L. / Allain, F.H.T.
CitationJournal: Science / Year: 2005
Title: Structure of PTB bound to RNA: specific binding and implications for splicing regulation
Authors: Oberstrass, F.C. / Auweter, S.D. / Erat, M. / Hargous, Y. / Henning, A. / Wenter, P. / Reymond, L. / Amir-Ahmady, B. / Pitsch, S. / Black, D.L. / Allain, F.H.T.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-R(*CP*UP*CP*UP*CP*U)-3'
A: Polypyrimidine tract-binding protein 1


Theoretical massNumber of molelcules
Total (without water)18,1682
Polymers18,1682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*CP*UP*CP*UP*CP*U)-3'


Mass: 1789.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#2: Protein Polypyrimidine tract-binding protein 1 / PTB / Heterogeneous nuclear ribonucleoprotein I / hnRNP I / 57 kDa RNA-binding protein PPTB-1


Mass: 16378.537 Da / Num. of mol.: 1 / Fragment: RBD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTB-1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL / References: UniProt: P26599

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1232D TOCSY
1313D 13C-separated NOESY
1423D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM PTB RBD2 15N, 13C; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl90% H2O/10% D2O
21.5mM PTB RBD2 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl90% H2O/10% D2O
31.5mM PTB RBD2 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl100% D2O
Sample conditionsIonic strength: 30mM / pH: 5.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Sparky3Goddarddata analysis
DYANA3.02Guentertstructure solution
Amber7Caserefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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