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- PDB-2jvo: Segmental isotope labeling of Npl3 -

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Basic information

Entry
Database: PDB / ID: 2jvo
TitleSegmental isotope labeling of Npl3
ComponentsNucleolar protein 3
KeywordsRNA BINDING PROTEIN / Protein / Nucleus / Phosphorylation / Ribonucleoprotein / Ribosome biogenesis / RNA-binding / rRNA processing
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 / simulated annealing
AuthorsSkrisovska, L. / Allain, F.H.-T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L
Authors: Skrisovska, L. / Allain, F.H.
History
DepositionSep 24, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)12,2931
Polymers12,2931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
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: 12292.843 Da / Num. of mol.: 1 / Fragment: RRM 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOP3, MTS1, NAB1, NPL3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ RIL / References: UniProt: Q01560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1922D 1H-1H TOCSY
11022D 1H-1H NOESY
11112D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] Npl3 RRM1, 1 mM [U-13C; U-15N] Npl3 RRM1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] Npl3 RRM1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNpl3-1 RRM1[U-15N]1
1 mMNpl3-2 RRM1[U-13C; U-15N]1
1 mMNpl3 RRM1[U-13C; U-15N]2
Sample conditionsIonic strength: 0.2 / pH: 7 / Pressure: ambient / Temperature: 303 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
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
ATNOS/CANDIDT. Herrmannautomated peak picking
ATNOS/CANDIDT. Herrmannautomated noe assignment
ATNOS/CANDIDT. Herrmannstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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