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- PDB-6c8u: Solution structure of Musashi2 RRM1 -

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Basic information

Entry
Database: PDB / ID: 6c8u
TitleSolution structure of Musashi2 RRM1
ComponentsRNA-binding protein Musashi homolog 2
KeywordsRNA BINDING PROTEIN / RNA recognition motif
Function / homology
Function and homology information


stem cell development / poly(U) RNA binding / RHOBTB2 GTPase cycle / central nervous system development / regulation of translation / intracellular membrane-bounded organelle / mRNA binding / RNA binding / identical protein binding / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsXing, M. / Lan, L. / Douglas, J.T. / Gao, P. / Hanzlik, R.P. / Xu, L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA178831 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA191785 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110761 United States
Department of Defense Breast Cancer Research Program Breakthrough Level IIBC151845 United States
Kansas Bioscience Authority Rising Star Award (to LX) United States
CitationJournal: Proteins / Year: 2019
Title: Crystal and solution structures of human oncoprotein Musashi-2 N-terminal RNA recognition motif 1.
Authors: Lan, L. / Xing, M. / Kashipathy, M. / Douglas, J. / Gao, P. / Battaile, K. / Hanzlik, R. / Lovell, S. / Xu, L.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: RNA-binding protein Musashi homolog 2


Theoretical massNumber of molelcules
Total (without water)13,1551
Polymers13,1551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein Musashi homolog 2 / Musashi-2


Mass: 13154.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RRM 1 domain (UNP residues 21-111) / Source: (gene. exp.) Homo sapiens (human) / Gene: MSI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DH6

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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
1111isotropic22D 1H-15N HSQC
122isotropic13D CBCA(CO)NH
132isotropic13D (H)CCH-TOCSY
1122isotropic13D (H)CCH-COSY
142isotropic13D HN(CA)CB
152isotropic13D HNCA
162isotropic13D HNCO
172isotropic13D HN(CO)CA
182isotropic13D HN(CA)CO
192isotropic13D 1H-15N NOESY
1102isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-90% 15N] MSI2-RRM1, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution20.7 mM [U-95% 13C; U-90% 15N] MSI2-RRM1, 95% H2O/5% D2O13C_15N sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMSI2-RRM1[U-90% 15N]1
0.7 mMMSI2-RRM1[U-95% 13C; U-90% 15N]2
Sample conditionsIonic strength: 150 mM NaCl mM / Label: CONDITION_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
NMRViewJohnson, One Moon Scientificpeak picking
TopSpin2.1pl6Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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