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- PDB-6soe: Mouse RBM20 RRM domain -

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Basic information

Entry
Database: PDB / ID: 6soe
TitleMouse RBM20 RRM domain
ComponentsRNA-binding protein 20
KeywordsRNA BINDING PROTEIN / alternative splicing
Function / homology
Function and homology information


heart formation / splicing factor binding / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / pre-mRNA intronic binding / positive regulation of RNA splicing / RNA splicing / cytoplasmic ribonucleoprotein granule ...heart formation / splicing factor binding / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / pre-mRNA intronic binding / positive regulation of RNA splicing / RNA splicing / cytoplasmic ribonucleoprotein granule / mRNA processing / mRNA binding / RNA binding / zinc ion binding / nucleus
Similarity search - Function
RBM20, RNA recognition motif / RNA-binding protein 20 / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 20
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMackereth, C.D. / Upadhyay, S.K.
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of UCUU RNA motif recognition by splicing factor RBM20.
Authors: Upadhyay, S.K. / Mackereth, C.D.
#1: Journal: Biorxiv / Year: 2019
Title: Structural basis of UCUU RNA motif recognition by splicing factor RBM20
Authors: Mackereth, C.D. / Upadhyay, S.K.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 20


Theoretical massNumber of molelcules
Total (without water)12,5721
Polymers12,5721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7150 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RNA-binding protein 20 / RNA-binding motif protein 20


Mass: 12571.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbm20 / Plasmid: pET-His1a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): lysY / References: UniProt: Q3UQS8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic23D HNCA
151isotropic23D HN(CA)CB
161isotropic23D CBCA(CO)NH
171isotropic22D 1H-13C HSQC aliphatic
181isotropic23D H(C)(CO)NH-TOCSY
191isotropic23D (H)C(CO)NH-TOCSY
1101isotropic23D (H)CCH-TOCSY
1111isotropic13D (H)CCH-TOCSY
1124isotropic12D 1H-13C HSQC CT
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic
1163isotropic22D 1H-13C HSQC aromatic
1172isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1400 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C,15N-labelled mouse RBM20 (residue 513-621)13C15N_H2O90% H2O/10% D2O
solution2500 uM Mouse RBM20 RRM domain, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2Onatural abundance mouse RBM20 (residue 513-621)unlabelled_H2O90% H2O/10% D2O
solution3170 uM [U-99% 13C] Mouse RBM20 RRM domain, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100% D2O13C-labelled mouse RBM20 (residue 513-621)13C_D2O100% D2O
solution4100 uM [U-10% 13C; U-99% 15N] Mouse RBM20 RRM domain, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O10%-13C,15N-labelled mouse RBM20 (residue 513-621)10%C15N_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMMouse RBM20 RRM domain[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
500 uMMouse RBM20 RRM domainnatural abundance2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
170 uMMouse RBM20 RRM domain[U-99% 13C]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
100 uMMouse RBM20 RRM domain[U-10% 13C; U-99% 15N]4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO7001TXI
Bruker AVANCE IIIBrukerAVANCE III8002cryoprobe TCI

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinalDetails
simulated annealing4ARIA 2.3
simulated annealing5CNS 1.2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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