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- PDB-2kvi: Structure of Nab3 RRM -

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Basic information

Entry
Database: PDB / ID: 2kvi
TitleStructure of Nab3 RRM
ComponentsNuclear polyadenylated RNA-binding protein 3
KeywordsRNA BINDING PROTEIN / Nab3 / RNA-binding motif / RRM / transcription termination / Nucleus / Phosphoprotein / RNA-binding
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 / tRNA 3'-end processing / snRNA 3'-end processing / CUT catabolic process / nuclear mRNA surveillance / mRNA 3'-end processing ...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 / tRNA 3'-end processing / snRNA 3'-end processing / CUT catabolic process / nuclear mRNA surveillance / mRNA 3'-end processing / SUMOylation of RNA binding proteins / 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
Nuclear polyadenylated RNA-binding protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsPergoli, R. / Kubicek, K. / Hobor, F. / Pasulka, J. / Stefl, R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Solution structure and RNA-binding study of RNA-recognition motif of Nab3
Authors: Pergoli, R. / Hobor, F. / Kubicek, K. / Pasulka, J. / Stefl, R.
History
DepositionMar 15, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear polyadenylated RNA-binding protein 3


Theoretical massNumber of molelcules
Total (without water)10,9921
Polymers10,9921
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear polyadenylated RNA-binding protein 3


Mass: 10992.458 Da / Num. of mol.: 1 / Fragment: RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NAB3, HMD1, YPL190C / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P38996

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HCACO
1313D CBCA(CO)NH
1413D HN(CA)CB
1512D 1H-13C HSQC
1613D 1H-13C NOESY
1713D 1H-15N NOESY
1813D HNHA
1913D (H)CCH-TOCSY
11012D HB(CB)(CGCD)HD

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Sample preparation

DetailsContents: 2.5 mM [U-99% 13C; U-99% 15N] RNA-binding protein-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2.5 mM / Component: RNA-binding protein-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.3 / pH: 8 / Pressure: 1 atm / 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
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpin2.1Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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