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- PDB-1sjr: NMR Structure of RRM2 from Human Polypyrimidine Tract Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 1sjr
TitleNMR Structure of RRM2 from Human Polypyrimidine Tract Binding Protein Isoform 1 (PTB1)
ComponentsPolypyrimidine tract-binding protein 1
KeywordsRNA BINDING PROTEIN / extended BABBAB motif
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 RNA splicing / regulation of cell differentiation ...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 RNA splicing / regulation of cell differentiation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of neuron differentiation / positive regulation of protein dephosphorylation / mRNA Splicing - Major Pathway / neurogenesis / RNA splicing / mRNA processing / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / 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
Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Hybrid distance geometry, simulated annealing
Model type detailsminimized average
AuthorsSimpson, P.J. / Monie, T.P. / Szendroi, A. / Davydova, N. / Tyzack, J.K. / Conte, M.R. / Read, C.M. / Cary, P.D. / Svergun, D.I. / Konarev, P.V. ...Simpson, P.J. / Monie, T.P. / Szendroi, A. / Davydova, N. / Tyzack, J.K. / Conte, M.R. / Read, C.M. / Cary, P.D. / Svergun, D.I. / Konarev, P.V. / Petoukhov, M.V. / Curry, S. / Matthews, S.J.
CitationJournal: Structure / Year: 2004
Title: Structure and RNA Interactions of the N-Terminal RRM Domains of PTB
Authors: Simpson, P.J. / Monie, T.P. / Szendroi, A. / Davydova, N. / Tyzack, J.K. / Conte, M.R. / Read, C.M. / Cary, P.D. / Svergun, D.I. / Konarev, P.V. / Curry, S. / Matthews, S.J.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polypyrimidine tract-binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,7581
Polymers17,7581
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)16 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Polypyrimidine tract-binding protein 1 / PTB / Heterogeneous nuclear ribonucleoprotein I / hnRNP I / 57 kDa RNA-binding protein PPTB-1


Mass: 17758.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP1, PTB / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 (Qiagen) / References: UniProt: P26599

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.25 mM PTB1-2, U-15N, 13C, 50 mM Na phosphate buffer, 100 mM NaCl, 10 mM DTT, 2 mM NaN3,10% D2O
Solvent system: 10% D2O
Sample conditionsIonic strength: 0.3 M / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Biospincollection
NMRPipe1Delaglio, F.processing
NMRView4.1.3Johnson, B. and Blevins, R.data analysis
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: Hybrid distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 16

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