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- PDB-2rs2: 1H, 13C, and 15N Chemical Shift Assignments for Musashi1 RBD1:r(G... -

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Basic information

Entry
Database: PDB / ID: 2rs2
Title1H, 13C, and 15N Chemical Shift Assignments for Musashi1 RBD1:r(GUAGU) complex
Components
  • RNA (5'-R(*GP*UP*AP*GP*U)-3')
  • RNA-binding protein Musashi homolog 1
KeywordsRNA BINDING PROTEIN/RNA / Musashi / Protein-RNA complex / RRM / RBD / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


: / poly(U) RNA binding / epithelial cell differentiation / response to hormone / central nervous system development / regulation of translation / single-stranded RNA binding / mRNA binding / identical protein binding / nucleus ...: / poly(U) RNA binding / epithelial cell differentiation / response to hormone / central nervous system development / regulation of translation / single-stranded RNA binding / mRNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA-binding protein Musashi homologue, RNA recognition motif 2 / 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 / RNA-binding protein Musashi homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsOhyama, T. / Nagata, T. / Tsuda, K. / Imai, T. / Okano, H. / Yamazaki, T. / Katahira, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions
Authors: Ohyama, T. / Nagata, T. / Tsuda, K. / Kobayashi, N. / Imai, T. / Okano, H. / Yamazaki, T. / Katahira, M.
History
DepositionJun 27, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: 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 / 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

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein Musashi homolog 1
B: RNA (5'-R(*GP*UP*AP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)13,7912
Polymers13,7912
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein RNA-binding protein Musashi homolog 1 / Musashi-1


Mass: 12203.913 Da / Num. of mol.: 1 / Fragment: RRM 1 domain, UNP residues 20-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msi1, Msi1h / Production host: Escherichia coli (E. coli) / References: UniProt: Q61474
#2: RNA chain RNA (5'-R(*GP*UP*AP*GP*U)-3')


Mass: 1586.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA

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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-13C HSQC
1312D 1H-1H TOCSY
1412D DQF-COSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D CBCA(CO)NH
11113D HBHA(CO)NH
11213D (H)CCH-TOCSY
11313D HN(CO)CA
11412D 13C-15N [f1,f2]-filtered NOESY
11512D 13C-15N [f2]-filtered NOESY

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Sample preparation

DetailsContents: 300 uM [U-13C; U-15N] Msi1 RBD1-1, 300 uM RNA-2, 20 mM MES-3, 5 mM DTT-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMMsi1 RBD1-1[U-13C; U-15N]1
300 uMRNA-21
20 mMMES-31
5 mMDTT-41
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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