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- PDB-2l41: Nab3 RRM - UCUU complex -

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Basic information

Entry
Database: PDB / ID: 2l41
TitleNab3 RRM - UCUU complex
Components
  • RNA (5'-R(P*UP*CP*UP*U)-3')
  • RRM domain from Nuclear polyadenylated RNA-binding protein 3RNA recognition motif
KeywordsRNA BINDING PROTEIN/RNA / Nab3 RRM / UCUU oligonucleotide / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance ...transcription regulatory region RNA binding / antisense RNA transcript catabolic process / Nrd1 complex / sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, exosome-dependent / snRNA 3'-end processing / tRNA 3'-end processing / CUT catabolic process / : / nuclear mRNA surveillance / : / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nab3, RNA recognition motif / Anticodon-binding domain superfamily / 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 ...Nab3, RNA recognition motif / Anticodon-binding domain superfamily / 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
RNA / Nuclear polyadenylated RNA-binding protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsStefl, R. / Pergoli, R. / Hobor, F. / Kubicek, K. / Zimmermann, M. / Pasulka, J. / Hofr, C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein
Authors: Hobor, F. / Pergoli, R. / Kubicek, K. / Hrossova, D. / Bacikova, V. / Zimmermann, M. / Pasulka, J. / Hofr, C. / Vanacova, S. / Stefl, R.
History
DepositionSep 28, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3May 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: RRM domain from Nuclear polyadenylated RNA-binding protein 3
B: RNA (5'-R(P*UP*CP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)10,0082
Polymers10,0082
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 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RRM domain from Nuclear polyadenylated RNA-binding protein 3 / RNA recognition motif / RRM domain from Nab3


Mass: 8829.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NAB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P38996
#2: RNA chain RNA (5'-R(P*UP*CP*UP*U)-3')


Mass: 1178.722 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNHA
1713D (H)CCH-TOCSY
1812D HB(CB)(CGCD)HD
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11112D F1 filtered F2 filtered
11212D F1 filtered F2 edited

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Sample preparation

DetailsContents: 2.5mM [U-99% 13C; U-99% 15N] Nab3 RRM-1, 2.5mM RNA-2, 50mM sodium phosphate buffer(pH 7.5)-3, 150mM sodium chloride-4, 10mM beta-mercaptoethanol-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMNab3 RRM-1[U-99% 13C; U-99% 15N]1
2.5 mMRNA-21
50 mMsodium phosphate buffer(pH 7.5)-31
150 mMsodium chloride-41
10 mMbeta-mercaptoethanol-51
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospincollection
Sparky3Goddardchemical shift assignment
Sparky3Goddarddata analysis
Sparky3Goddardpeak picking
MOLMOLKoradi, Billeter and Wuthrichdata analysis
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
WHAT IFVrienddata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Structures refined in explicit solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20 / Representative conformer: 1

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