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- PDB-2la4: NMR structure of the C-terminal RRM domain of poly(U) binding 1 -

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Basic information

Entry
Database: PDB / ID: 2la4
TitleNMR structure of the C-terminal RRM domain of poly(U) binding 1
ComponentsNuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
KeywordsRNA BINDING PROTEIN / RRM / RNA recognition / Stress granules / Nucleus / RNA-binding / Transcription
Function / homology
Function and homology information


poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / stress granule assembly / regulation of mRNA stability / P-body / cytoplasmic stress granule / mRNA binding / nucleus / cytoplasm
Similarity search - Function
RNA recognition motif domain, eukaryote / RNA recognition motif / 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 ...RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsSantiveri, C.M. / Mirassou, Y. / Rico-Lastres, P. / Martinez-Lumbreras, S. / Perez-Canadillas, J.M.
CitationJournal: Plos One / Year: 2011
Title: Pub1p C-terminal RRM domain interacts with Tif4631p through a conserved region neighbouring the Pab1p binding site
Authors: Santiveri, C.M. / Mirassou, Y. / Rico-Lastres, P. / Martinez-Lumbreras, S. / Perez-Canadillas, J.M.
History
DepositionMar 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1


Theoretical massNumber of molelcules
Total (without water)11,2961
Polymers11,2961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 / ARS consensus-binding protein ACBP-60 / Poly uridylate-binding protein / Poly(U)-binding protein


Mass: 11295.882 Da / Num. of mol.: 1 / Fragment: C-terminal RRM domain, residues 315-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32588

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1213D 1H-15N NOESY 2D 1H-15N HSQC
1343D HNCO
1443D HN(CA)CO
1543D HNCA
1643D HN(CO)CA
1743D CBCA(CO)NH
1843D CBCANH
1943D HC -TOCSY
11032D 1H-1H NOESY
11122D 1H-1H TOCSY
11232D 1H-1H TOCSY
11312D 1H-15N HSQC
11442D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3mM [U-99% 15N] PUB1 RRM3-1, 25mM potassium phosphate-2, 25mM sodium chloride-3, 0.5mM DTT-4, 0.01mM DSS-5, 90% H2O/10% D2O90% H2O/10% D2O
20.3mM PUB1 RRM3-6, 25mM potassium phosphate-7, 25mM sodium chloride-8, 0.5mM DTT-9, 0.01mM DSS-10, 90% H2O/10% D2O90% H2O/10% D2O
30.3mM PUB1 RRM3-11, 25mM potassium phosphate-12, 25mM sodium chloride-13, 0.5mM DTT-14, 0.1mM DSS-15, 100% D2O100% D2O
40.3mM [U-99% 13C; U-99% 15N] PUB1 RRM3-16, 25mM potassium phosphate-17, 25mM sodium chloride-18, 0.5mM DTT-19, 0.1mM DSS-20, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPUB1 RRM3-1[U-99% 15N]1
25 mMpotassium phosphate-21
25 mMsodium chloride-31
0.5 mMDTT-41
0.01 mMDSS-51
0.3 mMPUB1 RRM3-62
25 mMpotassium phosphate-72
25 mMsodium chloride-82
0.5 mMDTT-92
0.01 mMDSS-102
0.3 mMPUB1 RRM3-113
25 mMpotassium phosphate-123
25 mMsodium chloride-133
0.5 mMDTT-143
0.1 mMDSS-153
0.3 mMPUB1 RRM3-16[U-99% 13C; U-99% 15N]4
25 mMpotassium phosphate-174
25 mMsodium chloride-184
0.5 mMDTT-194
0.1 mMDSS-204
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TALOSCORNILESCU, DELAGLIOrefinement
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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