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- PDB-2osr: NMR Structure of RRM-2 of Yeast NPL3 Protein -

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Basic information

Entry
Database: PDB / ID: 2osr
TitleNMR Structure of RRM-2 of Yeast NPL3 Protein
ComponentsNucleolar protein 3
KeywordsRNA BINDING PROTEIN / Npl3 / RRM / SR protein / mRNA / RNA-binding
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / poly(A) binding / RNA polymerase II complex binding / translational termination / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / ribosome biogenesis / negative regulation of translation ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / eukaryotic initiation factor 4G binding / poly(A) binding / RNA polymerase II complex binding / translational termination / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / ribosome biogenesis / negative regulation of translation / ribonucleoprotein complex / mRNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Npl3, RNA recognition motif 1 / 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
Serine/arginine (SR)-type shuttling mRNA binding protein NPL3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDeka, P. / Bucheli, M. / Skrisovska, L. / Allain, F.H. / Moore, C. / Buratowski, S. / Varani, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals.
Authors: Deka, P. / Bucheli, M.E. / Moore, C. / Buratowski, S. / Varani, G.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: Nucleolar protein 3


Theoretical massNumber of molelcules
Total (without water)9,9641
Polymers9,9641
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleolar protein 3 / Mitochondrial targeting suppressor 1 protein / Nuclear polyadenylated RNA-binding protein 1


Mass: 9964.140 Da / Num. of mol.: 1 / Fragment: RRM 2 domain (residues 194-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOP3, MTS1, NAB1, NPL3 / Plasmid: pET-151 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY

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Sample preparation

Sample conditionsIonic strength: 20mM Potassium phosphate, 20mM potassium chloride
pH: 6.5 / Pressure: 1 atm / Temperature: 298 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 DMXBrukerDMX5001
Bruker AVANCEBrukerAVANCE7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERT, P. ET AL.refinement
CYANA2.1GUNTERT, P. ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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