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- PDB-2evz: Structure of RNA Binding Domains 3 and 4 of Polypyrimidine Tract ... -

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Basic information

Entry
Database: PDB / ID: 2evz
TitleStructure of RNA Binding Domains 3 and 4 of Polypyrimidine Tract Binding Protein
ComponentsPolypyrimidine tract-binding protein 1
KeywordsRNA BINDING PROTEIN / ALPHA-BETA SANDWICH
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 cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome ...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 cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of protein dephosphorylation / RNA splicing / mRNA Splicing - Major Pathway / 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
Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsAllain, F.H. / Auweter, S.D.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling
Authors: Vitali, F. / Henning, A. / Oberstrass, F.C. / Hargous, Y. / Auweter, S.D. / Erat, M. / Allain, F.H.
History
DepositionNov 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 22, 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
A: Polypyrimidine tract-binding protein 1


Theoretical massNumber of molelcules
Total (without water)25,2671
Polymers25,2671
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 / 30structures with the least restraint violations
RepresentativeModel #1lowest energy

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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: 25266.867 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAINS 3 AND 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP1, PTB / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)c+RIL / References: UniProt: P26599

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112HNCA
122HN(CO)CA
132CBCA(CO)NH
142HN(CA)CB
1513D 15N-separated NOESY
1643D 13C-separated NOESY
174(H)CCH-TOCSY
1832D NOESY
1952D F1-edited, F2-fitered NOESY
11053D 13C-separated half-filtered NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM PTB RBD34 15N; 20mM NaCl; 10mM sodium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
21mM PTB RBD34 15N, 13C; 20mM NaCl; 10mM sodium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
31mM PTB RBD34 15N; 20mM NaCl; 10mM sodium phosphate; 100% D2O100% D2O
41mM PTB RBD34 15N, 13C; 20mM NaCl; 10mM sodium phosphate; 100% D2O100% D2O
51mM PTB RBD3 15N, 13C, RBD4 unlabeled; 20mM NaCl; 10mM sodium phosphate; 100% D2O100% D2O
61mM PTB RBD3 unlabeled, RBD4 13C, 15N; 20mM NaCl; 10mM sodium phosphate; 100% D2O100% D2O
Sample conditionsIonic strength: 20mM NaCl, 10mM Na-phosphate / pH: 6.5 / Pressure: 1 atm / 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 AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Peter Guentertstructure solution
Amber7David A. Caserefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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