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- PDB-7eb1: Solution NMR structure of the RRM domain of RNA binding protein R... -

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Basic information

Entry
Database: PDB / ID: 7eb1
TitleSolution NMR structure of the RRM domain of RNA binding protein RBM3 from homo sapiens
ComponentsRNA-binding protein 3
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif (RRM) / RNA Binding Motif 3 (RBM3)
Function / homology
Function and homology information


positive regulation of mRNA splicing, via spliceosome / ribosomal large subunit binding / RNA processing / positive regulation of translation / spliceosomal complex / regulation of translation / dendrite / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
RBM3/CIRBP, RNA recognition motif / 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
Similarity search - Domain/homology
RNA-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBoral, S. / Roy, S. / Basak, A.J. / Maiti, S. / Lee, W. / De, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR34319/MED/29/1488/2019 India
Department of Science & Technology (DST, India)SR/WOS-A/LS-659/2016 India
CitationJournal: Febs J. / Year: 2022
Title: Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.
Authors: Roy, S. / Boral, S. / Maiti, S. / Kushwaha, T. / Basak, A.J. / Lee, W. / Basak, A. / Gholap, S.L. / Inampudi, K.K. / De, S.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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
A: RNA-binding protein 3


Theoretical massNumber of molelcules
Total (without water)9,2861
Polymers9,2861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 3 / RNA-binding motif protein 3 / RNPL


Mass: 9286.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM3, RNPL / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P98179

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
123isotropic12D 1H-15N HSQC
143isotropic12D 1H-13C HSQC
154isotropic12D 1H-13C HSQC
163isotropic13D CBCA(CO)NH
173isotropic13D HN(CA)CB
183isotropic13D HNCO
193isotropic13D HN(CA)CO
1103isotropic13D C(CO)NH
1113isotropic13D HBHA(CO)NH
1123isotropic13D (H)CCH-TOCSY
1132isotropic13D 1H-15N TOCSY
1143isotropic13D 1H-13C NOESY
1152isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution21.0 mM [U-100% 15N] RNA Binding Motif 3 (RBM3) protein, 93% H2O/7% D2O15N_sample93% H2O/7% D2O
solution30.6 mM [U-100% 13C; U-100% 15N] RNA Binding Motif 3 (RBM3) protein, 93% H2O/7% D2O13C_sample93% H2O/7% D2O
solution40.7 mM [U-10% 13C; U-100% 15N] RNA Binding Motif 3 (RBM3) protein, 93% H2O/7% D2O10%_13C_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRNA Binding Motif 3 (RBM3) protein[U-100% 15N]2
0.6 mMRNA Binding Motif 3 (RBM3) protein[U-100% 13C; U-100% 15N]3
0.7 mMRNA Binding Motif 3 (RBM3) protein[U-10% 13C; U-100% 15N]4
Sample conditionsDetails: 10 mM Phosphate buffer, 200 mM NaCl / Ionic strength: 1 Not defined / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
NMRFAM-SPARKYWoonghee Leepeak picking
NMRFAM-SPARKYWoonghee Leechemical shift assignment
PONDEROSA-C/SWoonghee Leestructure calculation
PONDEROSALee, W., Stark, J.L., and Markley, J.L.refinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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