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- PDB-2mju: Solution structure of a C terminal fragment of the neuronal isofo... -

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Basic information

Entry
Database: PDB / ID: 2mju
TitleSolution structure of a C terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB)
ComponentsPolypyrimidine tract-binding protein 2
KeywordsSPLICING / nPTB
Function / homology
Function and homology information


regulation of neural precursor cell proliferation / mRNA splice site recognition / negative regulation of RNA splicing / regulation of RNA splicing / spliceosomal complex / mRNA binding / RNA binding / nucleus
Similarity search - Function
PTBP2, RNA recognition motif 3 / PTBP2, RNA recognition motif 4 / PTBP2, RNA recognition motif 1 / 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 ...PTBP2, RNA recognition motif 3 / PTBP2, RNA recognition motif 4 / PTBP2, RNA recognition motif 1 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsEsteve, V. / Blatter, M. / Allain, F.H.-T.
CitationJournal: PeerJ / Year: 2014
Title: Solution and crystal structures of a C-terminal fragment of the neuronal isoform of the polypyrimidine tract binding protein (nPTB).
Authors: Joshi, A. / Esteve, V. / Buckroyd, A.N. / Blatter, M. / Allain, F.H. / Curry, S.
History
DepositionJan 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 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_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 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: Polypyrimidine tract-binding protein 2


Theoretical massNumber of molelcules
Total (without water)22,9191
Polymers22,9191
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 / 250structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Polypyrimidine tract-binding protein 2 / Neural polypyrimidine tract-binding protein / Neurally-enriched homolog of PTB / PTB-like protein


Mass: 22919.209 Da / Num. of mol.: 1 / Fragment: RRM34, UNP residues 325-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP2, NPTB, PTB, PTBLP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(+) / References: UniProt: Q9UKA9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1822D 1H-1H TOCSY
1922D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] nPTB, 20 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] nPTB, 20 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMnPTB-1[U-100% 13C; U-100% 15N]1
20 mMsodium chloride-21
10 mMsodium phosphate-31
1 mMnPTB-4[U-100% 15N]2
20 mMsodium chloride-52
10 mMsodium phosphate-62
Sample conditionsIonic strength: 0.03 / pH: 5.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3Guntert, Mumenthaler and Wuthrichnoe assignment
TopSpin3.1Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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