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- PDB-2lq5: NMR structure of the RNA binding motif 39 (RBM39) from Mus musculus -

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Basic information

Entry
Database: PDB / ID: 2lq5
TitleNMR structure of the RNA binding motif 39 (RBM39) from Mus musculus
ComponentsRNA-binding protein 39
KeywordsRNA BINDING PROTEIN / RNA binding domain / Structural Genomics / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / RHOG GTPase cycle / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / nucleoplasm
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 39
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsSerrano, P. / Dutta, S.K. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of the RNA binding motif 39 (RBM39) from Mus musculus
Authors: Serrano, P. / Dutta, S.K. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionFeb 23, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)12,5161
Polymers12,5161
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 / 80target function
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 39 / Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA- ...Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Transcription coactivator CAPER


Mass: 12516.202 Da / Num. of mol.: 1 / Fragment: RRM 3 domain residues 418-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbm39, Caper, Rnpc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8VH51

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-15N NOESY
1413D 1H-13C NOESY aromatic
1514D APSY HACANH
1615D APSY CBCA(CO)NH
1715D APSY (HA)CA(CO)NH
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.2 mM [U-95% 13C; U-95% 15N] protein, 4.5 mM sodium azide, 50 mM sodium chloride, 25 mM sodium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-95% 13C; U-95% 15N]1
4.5 mMsodium azide-21
50 mMsodium chloride-31
25 mMsodium phosphate-41
Sample conditionsIonic strength: 0.083 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospindata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
UNIOUnio Herrmann Wuthrichchemical shift assignment
UNIOUnio Herrmann Wuthrichstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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