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- PDB-2aym: Solution Structure of Drosophila melanogaster SNF RBD2 -

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Basic information

Entry
Database: PDB / ID: 2aym
TitleSolution Structure of Drosophila melanogaster SNF RBD2
ComponentsU1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / SNF RBD2 / RNA binding / RNA splicing / solution structure
Function / homology
Function and homology information


primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / female germ-line sex determination / mRNA Splicing - Major Pathway / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / regulation of alternative mRNA splicing, via spliceosome ...primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / female germ-line sex determination / mRNA Splicing - Major Pathway / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / regulation of alternative mRNA splicing, via spliceosome / precatalytic spliceosome / oogenesis / 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, molecular dynamics
AuthorsCui, G. / Li, C. / Jin, C. / Xia, B.
CitationJournal: To be published
Title: Solution Structure of Drosophila melanogaster SNF RBD2
Authors: Cui, G. / Li, C. / Jin, C. / Xia, B.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: 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
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
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: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)9,5201
Polymers9,5201
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 / SNF / U1 snRNP protein A / U1-A / Sex determination protein snf


Mass: 9519.945 Da / Num. of mol.: 1 / Fragment: SNF RBD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET-28(a+) / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techaniques

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Sample preparation

DetailsContents: 1mM SNF RBD2 U-15N,13C; 50mM phosphate buffer NA; 1mM EDTA; 50mM NaCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 250mM / pH: 7.2 / 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
XwinNMR3.5Brukercollection
NMRPipe2.1Frank Delaglioprocessing
NMRView5Bruce Johnsondata analysis
CYANA1.0.6Peter Guntertstructure solution
Amber7David Caserefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structure was based on total 3828 restraints. 3715 are NOE derived distance constraints, 61 are dihedral angle restraints, 52 are distance restraints from hydrogen bonds.
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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