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- PDB-2fho: NMR solution structure of the human spliceosomal protein complex ... -

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Basic information

Entry
Database: PDB / ID: 2fho
TitleNMR solution structure of the human spliceosomal protein complex p14-SF3b155
Components
  • spliceosomal protein SF3b155
  • spliceosomal protein p14
KeywordsRNA BINDING PROTEIN / RRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / B-WICH complex positively regulates rRNA expression / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / 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 / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor 3B subunit 1 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained ENERGY MINIMIZATION
AuthorsKuwasako, K. / Dohmae, N. / Inoue, M. / Shirouzu, M. / Guntert, P. / Seraphin, B. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: NMR solution structure of the human spliceosomal protein complex p14-SF3b155
Authors: Kuwasako, K. / Dohmae, N. / Inoue, M. / Shirouzu, M. / Guntert, P. / Seraphin, B. / Muto, Y. / Yokoyama, S.
History
DepositionDec 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spliceosomal protein SF3b155
B: spliceosomal protein p14


Theoretical massNumber of molelcules
Total (without water)15,6512
Polymers15,6512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide spliceosomal protein SF3b155 / spliceosomal protein SF3b155 / Spliceosome associated protein 155 / SAP 155 / SF3b155 / Pre-mRNA ...spliceosomal protein SF3b155 / Spliceosome associated protein 155 / SAP 155 / SF3b155 / Pre-mRNA splicing factor SF3b 155 kDa subunit


Mass: 5502.108 Da / Num. of mol.: 1 / Fragment: residues in database 379-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3b155 / Plasmid: PGEX6P-1-SF3B155(379-424)-HIS6-P14(8-93) / Production host: Escherichia coli (E. coli) / References: UniProt: O75533
#2: Protein spliceosomal protein p14 / spliceosomal protein p14 / SF3B 14 kDa subunit


Mass: 10148.584 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p14 / Plasmid: PGEX6P-1-SF3B155(379-424)-HIS6-P14(8-93) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 20mM Sodium Phosphate buffer (pH 6.5), 100mM NaCl, 1mM d-DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 308 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
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, Fprocessing
NMRView5.0.4Johnson, B.Adata analysis
KUJIRA0.8995Kobayashi, Ndata analysis
CYANA2.1Guntert, Pstructure solution
OPALp1.4Koradi, R.structure solution
CYANA2.1Guntert, Prefinement
OPALp1.4Koradi, R.refinement
RefinementMethod: torsion angle dynamics, restrained ENERGY MINIMIZATION
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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