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- PDB-2k3k: Solution structure of Drosophila melanogaster SNF RBD1 -

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Basic information

Entry
Database: PDB / ID: 2k3k
TitleSolution structure of Drosophila melanogaster SNF RBD1
ComponentsU1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / SNF RBD1 / RNA binding / RNA splicing / solution structure / mRNA processing / mRNA splicing / Nucleus / Ribonucleoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / mRNA Splicing - Major Pathway / female germ-line sex determination / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / oogenesis ...primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / mRNA Splicing - Major Pathway / female germ-line sex determination / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / oogenesis / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / U2 snRNA binding / U1 snRNA binding / catalytic step 2 spliceosome / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / mRNA binding / protein-containing complex / identical protein binding / nucleus
Similarity search - Function
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
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
Model detailsDrosophila homolog of mammalian U1A and U2B
AuthorsLiu, C. / Cui, G. / Hu, J. / Jin, C. / Xia, B.
CitationJournal: To be Published
Title: Structural and Functional Studies of RNA Splicing Factor Sans-Fille by Multidimentional NMR Spectroscopy
Authors: Hu, J. / Cui, G. / Li, C. / Liu, C. / Jin, C. / Wang, J. / Xia, B.
History
DepositionMay 12, 2008Deposition site: BMRB / Processing site: RCSB
SupersessionJun 3, 2008ID: 2FJJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,9731
Polymers11,9731
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1-A / Sex determination protein snf


Mass: 11973.117 Da / Num. of mol.: 1 / Fragment: RRM1 domain (UNP residues 1-98)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET-21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(de3)plyss / References: UniProt: P43332

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Drosophila homolog of mammalian U1A and U2B
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] SNF RBD1, 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSNF RBD1[U-100% 13C; U-100% 15N]1
50 mMpotassium phosphate1
50 mMsodium chloride1
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber7David Caserefinement
CYANA1.06Peter Guntertstructure solution
NMRView5Bruce Johnsondata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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