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- PDB-5obn: NMR solution structure of U11/U12 65K protein's C-terminal RRM do... -

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Basic information

Entry
Database: PDB / ID: 5obn
TitleNMR solution structure of U11/U12 65K protein's C-terminal RRM domain (381-516)
ComponentsRNA-binding protein 40
KeywordsSPLICING / Minor spliceosome / RNA binding
Function / homology
Function and homology information


U12 snRNA binding / U12-type spliceosomal complex / mRNA Splicing - Minor Pathway / pre-mRNA intronic binding / RNA splicing / mRNA splicing, via spliceosome / nucleoplasm / nucleus
Similarity search - Function
RBM40, RNA recognition motif 1 / RNA-binding region-containing protein RBM41/RNPC3 / 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 region-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsNorppa, A.J. / Kauppala, T.M. / Heikkinen, H.A. / Verma, B. / Iwai, H. / Frilander, M.J.
Funding support Finland, 7items
OrganizationGrant numberCountry
Academy of Finland277335 Finland
Academy of Finland140087 Finland
Academy of Finland278798 Finland
Biocenter Finland Finland
Sigrid Juselius Foundation Finland
Biocentrum Helsinki Finland
Integrative Life Science doctoral program Finland
CitationJournal: RNA / Year: 2018
Title: Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA.
Authors: Norppa, A.J. / Kauppala, T.M. / Heikkinen, H.A. / Verma, B. / Iwai, H. / Frilander, M.J.
History
DepositionJun 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 40


Theoretical massNumber of molelcules
Total (without water)15,7961
Polymers15,7961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
Representative

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Components

#1: Protein RNA-binding protein 40 / RNA-binding motif protein 40 / RNA-binding region-containing protein 3 / U11/U12 small nuclear ...RNA-binding motif protein 40 / RNA-binding region-containing protein 3 / U11/U12 small nuclear ribonucleoprotein 65 kDa protein / U11/U12-65K


Mass: 15796.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNPC3, KIAA1839, RBM40, RNP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LT9

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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
121isotropic22D 1H-13C HSQC
231isotropic13D HNCA
241isotropic13D HN(CA)CB
251isotropic13D HN(COCA)CB
161isotropic1HNCO
271isotropic1HN(CA)CO
291isotropic1CON
2101isotropic1CACO
1111isotropic1(H)CC(CO)NH
1121isotropic1H(CCO)NH
1131isotropic1HBHA(CO)NH
1141isotropic2(H)CCH-COSY
1161isotropic1CBCGCDHD
1171isotropic1CBCGCDCEHE
1181isotropic23D 1H-15N NOESY
1151isotropic23D 1H-13C NOESY aliphatic
1191isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O
Label: 15N13C / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.2 mM / Component: U11/U12 65K C-terminal RRM / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120.0 mMconditions_16.0 1 atm303.3 K
220.0 mMconditions_26.0 1 atm298.3 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

SoftwareName: AMBER / Version: 14 / Classification: refinement
NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CcpNmr Analysis2.4.1CCPNchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
TALOSNCornilescu, Delaglio and Baxstructure calculation
PSVS1.5Bhattacharya and Montelionedata analysis
TopSpin3.2Bruker Biospinprocessing
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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