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- PDB-5x3z: Solution structure of musashi1 RBD2 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 5x3z
TitleSolution structure of musashi1 RBD2 in complex with RNA
Components
  • RNA (5'-R(*GP*UP*AP*GP*U)-3')
  • RNA-binding protein Musashi homolog 1
KeywordsRNA BINDING PROTEIN/RNA / RNA-binding protein / 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 / 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
AuthorsIwaoka, R. / Nagata, T. / Tsuda, K. / Imai, T. / Okano, H. / Kobayashi, N. / Katahira, M.
Funding support Japan, 5items
OrganizationGrant numberCountry
JSPS15H01256 Japan
JSPS16H00833 Japan
JSPS16K14678 Japan
JSPS15H01634 Japan
JSPS26440026 Japan
CitationJournal: Molecules / Year: 2017
Title: Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA
Authors: Iwaoka, R. / Nagata, T. / Tsuda, K. / Imai, T. / Okano, H. / Kobayashi, N. / Katahira, M.
History
DepositionFeb 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: 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

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MolmilJmol/JSmol

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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)12,5322
Polymers12,5322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area6660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 10945.506 Da / Num. of mol.: 1 / Fragment: UNP residues 109-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msi1, Msi1h / Plasmid: pET15b / 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 / Source: (synth.) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY
151isotropic23D 1H-13C NOESY
161isotropic13D HNCO
171isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
191isotropic13D HNCA
1101isotropic13D HBHA(CO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] Msi1 RBD2, 300 uM RNA (5'-R(*GP*UP*AP*GP*U)-3'), 95% H2O/5% D2O
Label: 15N/13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMMsi1 RBD2[U-100% 13C; U-100% 15N]1
300 uMRNA (5'-R(*GP*UP*AP*GP*U)-3')natural abundance1
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
MAGROKobayashichemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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