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- PDB-5mf9: Solution structure of the RBM5 OCRE domain in complex with polypr... -

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Basic information

Entry
Database: PDB / ID: 5mf9
TitleSolution structure of the RBM5 OCRE domain in complex with polyproline SmN peptide.
Components
  • RNA-binding protein 5
  • Survival motor neuron protein
KeywordsSPLICING / OCRE / Poly proline binding domain / SmN / alternative splicing
Function / homology
Function and homology information


Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / spliceosomal snRNP assembly / RNA processing / Cajal body / mRNA Splicing - Major Pathway / spliceosomal complex ...Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / spliceosomal snRNP assembly / RNA processing / Cajal body / mRNA Splicing - Major Pathway / spliceosomal complex / DNA-templated transcription termination / mRNA splicing, via spliceosome / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / perikaryon / SARS-CoV-2 modulates host translation machinery / neuron projection / nuclear body / positive regulation of apoptotic process / negative regulation of cell population proliferation / axon / intracellular membrane-bounded organelle / mRNA binding / apoptotic process / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / G-patch domain / Tudor domain profile. / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Tudor domain / Tudor domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / 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 5 / Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMourao, A. / Sattler, M. / Bonnal, S. / Komal, S. / Warner, L. / Bordonne, R. / Valcarcel, J.
Funding support Germany, Spain, 4items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
German Research FoundationGRK1721 Germany
Banco de SantanderConsolider RNAREG, MICINN, AGAUR Spain
Spanish Ministry of Economy and CompetitivenessCentro de Excelencia Severo Ochoa 2013-2017, SEV-2012-0208 Spain
CitationJournal: Elife / Year: 2016
Title: Structural basis for the recognition ofspliceosomal SmN B B proteins by theRBM5 OCRE domain in splicing regulation
Authors: Mourao, A. / Bonnal, S. / Komal, S. / Warner, L. / Bordonne, R. / Valcarcel, J. / Sattler, M.
History
DepositionNov 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 31, 2018Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 5
B: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)8,5732
Polymers8,5732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1000 Å2
ΔGint-5 kcal/mol
Surface area5340 Å2
MethodPISA
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 5 / Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma ...Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma antigen NY-REN-9


Mass: 7436.785 Da / Num. of mol.: 1 / Fragment: UNP residues 451-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM5, H37, LUCA15 / Production host: Escherichia coli (E. coli) / References: UniProt: P52756
#2: Protein/peptide Survival motor neuron protein / Component of gems 1 / Gemin-1


Mass: 1136.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMN1, SMN, SMNT, SMN2, SMNC / Production host: Escherichia coli (E. coli) / References: UniProt: Q16637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D 1H-13C NOESY aliphatic
121isotropic33D 1H-13C HSQC aromatic
131isotropic12D 1H-15N HSQC
141isotropic32D 1H-1H NOESY
151isotropic23D HNCA
161isotropic23D CBCA(CO)NH
171isotropic23D HN(CA)CB
181isotropic23D HNCO
191isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solid
Contents: 2 mM [U-99% 15N] 15N, 2 mM [U-99% 13C; U-99% 15N] 13C_15N, 2 mM [U-13C; U-15N] unlabel, 90% H2O/10% D2O
Label: OCRE_SmN / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mM15N[U-99% 15N]1
2 mM13C_15N[U-99% 13C; U-99% 15N]1
2 mMunlabel[U-13C; U-15N]1
Sample conditionsIonic strength: 50 mM / Label: 15N_sample / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002cryoprobe
Bruker DRXBrukerDRX9003cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
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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