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- PDB-1uaw: Solution structure of the N-terminal RNA-binding domain of mouse ... -

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Basic information

Entry
Database: PDB / ID: 1uaw
TitleSolution structure of the N-terminal RNA-binding domain of mouse Musashi1
Componentsmouse-musashi-1
KeywordsRNA BINDING PROTEIN / RNP-type structure
Function / homology
Function and homology information


poly(U) RNA binding / response to hormone / epithelial cell differentiation / molecular condensate scaffold activity / single-stranded RNA binding / protein homodimerization activity / 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-binding protein Musashi homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMiyanoiri, Y. / Kobayashi, H. / Watanabe, M. / Ikeda, T. / Nagata, T. / Okano, H. / Uesugi, S. / Katahira, M.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes ...Title: Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics
Authors: Miyanoiri, Y. / Kobayashi, H. / Imai, T. / Watanabe, M. / Nagata, T. / Uesugi, S. / Okano, H. / Katahira, M.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Structure, Backbone Dynamics and Interactions with RNA of the C-terminal RNA-binding Domain of a Mouse Neural RNA-binding Protein, Musashi1.
Authors: Nagata, T. / Kanno, R. / Kurihara, Y. / Uesugi, S. / Imai, T. / Sakakibara, S. / Okano, H. / Katahira, M.
#2: Journal: Gene / Year: 1997
Title: Structural properties and RNA-binding activities of two RNA recognition motifs of a mouse neural RNA-binding protein, mouse-Musashi-1.
Authors: Kurihara, Y. / Nagata, T. / Imai, T. / Hiwatashi, A. / Horiuchi, M. / Sakakibara, S. / Katahira, M. / Okano, H. / Uesugi, S.
History
DepositionMar 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mouse-musashi-1


Theoretical massNumber of molelcules
Total (without water)8,7761
Polymers8,7761
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)15 / 103structures with the lowest energy
Representative

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Components

#1: Protein mouse-musashi-1


Mass: 8776.088 Da / Num. of mol.: 1 / Fragment: N-terminal RNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: neural stem / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61474

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1322D NOESY
1422D TOCSY
1532D NOESY
1632D TOCSY
173DQF-COSY
NMR detailsText: The structure was determined using 2D homonuclear and 3D 15N-edited heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM 15N labeled Musashi1 RBD1, 20mM sodium phosphate, 1.0mM sodium azide, 10mM deuterated DTT, small amounts of DSS95% H2O, 5.0% D2O
22.0mM Musashi1 RBD1, 20mM sodium phosphate, 1.0mM sodium azide, 10mM deuterated DTT, small amounts of DSS95% H2O, 5.0% D2O
32.0mM Musashi1 RBD1, 20mM sodium phosphate, 1.0mM sodium azide, 10mM deuterated DTT, small amounts of DSS100% D2O
Sample conditionsIonic strength: 0.0mM / pH: 6 / Pressure: 1.0atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8Brungerrefinement
CAPP/PIPP/STAPP4.2.5Garretdata analysis
XwinNMR2.6Brukerprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 103 / Conformers submitted total number: 15

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