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- PDB-2rt3: Solution structure of the second RRM domain of Nrd1 -

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Basic information

Entry
Database: PDB / ID: 2rt3
TitleSolution structure of the second RRM domain of Nrd1
ComponentsNegative regulator of differentiation 1
KeywordsRNA BINDING PROTEIN / Nrd1 / RNA-binding
Function / homology
Function and homology information


negative regulation of conjugation with cellular fusion / poly(U) RNA binding / cytoplasmic stress granule / mRNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / cytosol / cytoplasm
Similarity search - Function
Mrn1, RNA recognition motif 1 / Pre-mRNA-splicing factor Cwc2/Slt11 / 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 ...Mrn1, RNA recognition motif 1 / Pre-mRNA-splicing factor Cwc2/Slt11 / 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
Negative regulator of differentiation 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKobayashi, A. / Kanaba, T. / Mishima, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Structure of the second RRM domain of Nrd1, a fission yeast MAPK target RNA binding protein, and implication for its RNA recognition and regulation
Authors: Kobayashi, A. / Kanaba, T. / Satoh, R. / Fujiwara, T. / Ito, Y. / Sugiura, R. / Mishima, M.
History
DepositionApr 16, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Negative regulator of differentiation 1


Theoretical massNumber of molelcules
Total (without water)10,7931
Polymers10,7931
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Negative regulator of differentiation 1 / Multicopy suppressor of sporulation protein msa2


Mass: 10793.342 Da / Num. of mol.: 1 / Fragment: RRM2 domain, residues 188-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: nrd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09702

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HN(CA)CO
1513D HNCO
1613D H(CCO)NH
1713D C(CO)NH
1814D H(CCO)NH
1933D 1H-13C NOESY
11023D 1H-15N NOESY
11123D HNHB
11233D HA(CA)HB
11342D 1H-13C CT-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium phosphate-1, 100 mM sodium chloride-2, 1 mM TCEP-3, 0.1 mM EDTA-4, 1.0 mM [U-99% 13C; U-99% 15N] Nrd1 RRM2-5, 93% H2O/7% D2O93% H2O/7% D2O
250 mM potassium phosphate-6, 100 mM sodium chloride-7, 1 mM TCEP-8, 0.1 mM EDTA-9, 1.2 mM [U-99% 15N] Nrd1 RRM2-10, 93% H2O/7% D2O93% H2O/7% D2O
350 mM potassium phosphate-11, 100 mM sodium chloride-12, 1 mM TCEP-13, 0.1 mM EDTA-14, 1.0 mM [U-99% 13C; U-99% 15N] Nrd1 RRM2-15, 100% D2O100% D2O
450 mM potassium phosphate-16, 100 mM sodium chloride-17, 1 mM TCEP-18, 0.1 mM EDTA-19, 0.35 mM [U-10% 13C; U-99% 15N] Nrd1 RRM2-20, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-11
100 mMsodium chloride-21
1 mMTCEP-31
0.1 mMEDTA-41
1.0 mMNrd1 RRM2-5[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-62
100 mMsodium chloride-72
1 mMTCEP-82
0.1 mMEDTA-92
1.2 mMNrd1 RRM2-10[U-99% 15N]2
50 mMpotassium phosphate-113
100 mMsodium chloride-123
1 mMTCEP-133
0.1 mMEDTA-143
1.0 mMNrd1 RRM2-15[U-99% 13C; U-99% 15N]3
50 mMpotassium phosphate-164
100 mMsodium chloride-174
1 mMTCEP-184
0.1 mMEDTA-194
0.35 mMNrd1 RRM2-20[U-10% 13C; U-99% 15N]4
Sample conditionspH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AvanceIII / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
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 / Representative conformer: 1

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