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- PDB-5gvq: Solution structure of the first RRM domain of human spliceosomal ... -

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Basic information

Entry
Database: PDB / ID: 5gvq
TitleSolution structure of the first RRM domain of human spliceosomal protein SF3b49
ComponentsSplicing factor 3B subunit 4
KeywordsRNA BINDING PROTEIN / RRM / SF3b49 / SF3b145 / U2 snRNP / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


U2-type prespliceosome assembly / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / mRNA Splicing - Minor Pathway / spliceosomal complex ...U2-type prespliceosome assembly / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / mRNA Splicing - Minor Pathway / spliceosomal complex / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / mRNA processing / RNA binding / nucleoplasm / nucleus
Similarity search - Function
SF3B4, RNA recognition motif 2 / SF3B4, RNA recognition motif 1 / 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 ...SF3B4, RNA recognition motif 2 / SF3B4, RNA recognition motif 1 / 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
Splicing factor 3B subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. ...Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / Guntert, P. / Takahashi, S. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2017
Title: Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.
Authors: Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / ...Authors: Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / Guntert, P. / Takahashi, S. / Yokoyama, S. / Muto, Y.
History
DepositionSep 6, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 12, 2017ID: 1X5U
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 3B subunit 4


Theoretical massNumber of molelcules
Total (without water)11,3791
Polymers11,3791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Splicing factor 3B subunit 4 / spliceosomal protein SF3b49 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated ...spliceosomal protein SF3b49 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 11378.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B4, SAP49 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15427*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] human spliceosomal protein SF3b49, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: human spliceosomal protein SF3b49 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: condistions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AMBERCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
kujiraKobayashi Ndata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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