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- PDB-8b8s: Solution structure of tandem RRM1 and RRM2 domains of yeast NPL3 -

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Basic information

Entry
Database: PDB / ID: 8b8s
TitleSolution structure of tandem RRM1 and RRM2 domains of yeast NPL3
ComponentsSerine/arginine (SR)-type shuttling mRNA binding protein NPL3
KeywordsRNA BINDING PROTEIN / Serine/arginine (SR)-type mRNA binding protein / Paramagnetic relaxation enhancement (PRE) based solution NMR structure
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 / 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
Similarity search - Domain/homology
Serine/arginine (SR)-type shuttling mRNA binding protein NPL3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsKachariya, N. / Sattler, M. / Keil, P. / Strasser, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1935 Germany
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Authors: Keil, P. / Wulf, A. / Kachariya, N. / Reuscher, S. / Huhn, K. / Silbern, I. / Altmuller, J. / Keller, M. / Stehle, R. / Zarnack, K. / Sattler, M. / Urlaub, H. / Strasser, K.
#1: Journal: Biorxiv / Year: 2022
Title: Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA
Authors: Keil, P. / Wulf, A. / Kachariya, N. / Reuscher, S. / Huhn, K. / Silbern, I. / Altmuller, J. / Stehle, R. / Zarnack, K. / Sattler, M. / Urlaub, H. / Strasser, K.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 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: Serine/arginine (SR)-type shuttling mRNA binding protein NPL3


Theoretical massNumber of molelcules
Total (without water)18,2281
Polymers18,2281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/arginine (SR)-type shuttling mRNA binding protein NPL3 / Mitochondrial targeting suppressor 1 protein / Nuclear polyadenylated RNA-binding protein 1 / ...Mitochondrial targeting suppressor 1 protein / Nuclear polyadenylated RNA-binding protein 1 / Nuclear protein localization protein 3 / Polyadenylate-binding protein NPL3


Mass: 18228.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Uniprot
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NPL3, MTR13, MTS1, NAB1, NOP3, YDR432W, D9461.19 / Plasmid: pET family vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01560

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HCACO
161isotropic13D H(CCO)NH
171isotropic13D C(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1150 uM [U-100% 15N] RRM1,2 of NPL3, 90% H2O/10% D2Osample-190% H2O/10% D2O
solution21000 uM [U-100% 13C; U-100% 15N] RRM1,2 of NPL3, 90% H2O/10% D2Osample-190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMRRM1,2 of NPL3[U-100% 15N]1
1000 uMRRM1,2 of NPL3[U-100% 13C; U-100% 15N]2
Sample conditionsDetails: For PRE (Paramagnetic Relaxation Enhancement) NMR measurement, the IPSL (3-{2-Iodoacetamid}-PROXYL) spin label attached at defined positions on each RRM domain and 1H-15N HSQC spectra ...Details: For PRE (Paramagnetic Relaxation Enhancement) NMR measurement, the IPSL (3-{2-Iodoacetamid}-PROXYL) spin label attached at defined positions on each RRM domain and 1H-15N HSQC spectra recorded at oxidized and reduced state of the protein sample. The reduced state of the spectra measured by adding 10x molar excess of ascorbate in the sample.
Ionic strength: 70 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III9501Cryogenic cool probe
Bruker AVANCE IIIBrukerAVANCE III9002Cryogenic cool probe
Bruker AVANCE IIIBrukerAVANCE III8003Cryogenic cool probe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin3.5pl6Bruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.5.0CCPNchemical shift assignment
CcpNmr Analysis2.5.0CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The ensemble structures are based on total of 100 distance restrains derived from PRE experiments, where 69 and 31 are intra- and inter-domain restrains.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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