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- PDB-7q33: Solution structure of RBM39 RRM2 bound to 5'-AGCUUUG-3 -

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Basic information

Entry
Database: PDB / ID: 7q33
TitleSolution structure of RBM39 RRM2 bound to 5'-AGCUUUG-3
Components
  • RNA (5'-R(*AP*GP*CP*UP*UP*UP*G)-3')
  • RNA-binding protein 39
KeywordsRNA BINDING PROTEIN / RNA binding / RRM / extended RNA binding surface
Function / homology
Function and homology information


RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck ...RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / 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 / 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 / RNA-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCampagne, S. / Allain, F.H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR RNA and Diseases Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.
Authors: Campagne, S. / Jutzi, D. / Malard, F. / Matoga, M. / Romane, K. / Feldmuller, M. / Colombo, M. / Ruepp, M.D. / Allain, F.H.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 39
B: RNA (5'-R(*AP*GP*CP*UP*UP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,6392
Polymers12,6392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 39 / CAPER alpha / CAPERalpha / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA- ...CAPER alpha / CAPERalpha / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Splicing factor HCC1


Mass: 10441.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM39, HCC1, RNPC2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q14498
#2: RNA chain RNA (5'-R(*AP*GP*CP*UP*UP*UP*G)-3')


Mass: 2198.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)

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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
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
171isotropic33D 1H-15N NOESY
181isotropic33D 1H-13C NOESY aliphatic
191isotropic33D 1H-13C NOESY aromatic
1102isotropic22D F1FF2F NOESY
1112isotropic22D F2F NOESY
1122isotropic22D F2f TOCSY
1132isotropic33D 1H-13C NOESY aliphatic
1142isotropic33D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution110 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 1.2 mM 13C; 15N RBM39 RRM2, 1.2 mM AGCUUUG, 90% H2O/10% D2ORBM39-RRM2 13C 15N labelled in complex with AGCUUUUG NaPO4 10 mM pH6.5 NaCl 50 mM DTT 2 mMH2O90% H2O/10% D2O
solution210 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 1.2 mM 13C; 15N RBM39 RRM2, 1.2 mM AGCUUUG, 100% D2ORBM39-RRM2 13C 15N labelled in complex with AGCUUUUG NaPO4 10 mM pH6.5 NaCl 50 mM DTT 2 mMD20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMNaPO4natural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
1.2 mMRBM39 RRM213C; 15N1
1.2 mMAGCUUUGnatural abundance1
10 mMNaPO4natural abundance2
50 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
1.2 mMRBM39 RRM213C; 15N2
1.2 mMAGCUUUGnatural abundance2
Sample conditionsDetails: NaPO4 10 mM pH6.5 NaCl 50 mM DTT 2 mM / Ionic strength: 60 mM / Label: conditions_1 / pH: 6.5 / Pressure: ATM atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO7002
Bruker AVANCE III HDBrukerAVANCE III HD9003

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ATNOSThorstenpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3 / Details: SA in cartesian space
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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