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- PDB-2khc: Bruno RRM3+ -

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Basic information

Entry
Database: PDB / ID: 2khc
TitleBruno RRM3+
ComponentsTestis-specific RNP-type RNA binding protein
KeywordsRNA BINDING PROTEIN / RRM / RNA Recognition Motif / Bruno
Function / homology
Function and homology information


regulation of myofibril size / negative regulation of oskar mRNA translation / female germ-line stem cell population maintenance / positive regulation of exit from mitosis / positive regulation of stem cell differentiation / mRNA splice site recognition / P granule / sarcomere organization / regulation of alternative mRNA splicing, via spliceosome / oogenesis ...regulation of myofibril size / negative regulation of oskar mRNA translation / female germ-line stem cell population maintenance / positive regulation of exit from mitosis / positive regulation of stem cell differentiation / mRNA splice site recognition / P granule / sarcomere organization / regulation of alternative mRNA splicing, via spliceosome / oogenesis / germ cell development / mRNA 3'-UTR binding / nuclear membrane / negative regulation of translation / nuclear body / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
CELF1/2, 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
Testis-specific RNP-type RNA binding protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsLyon, A.M. / Reveal, B.S. / Macdonald, P.M. / Hoffman, D.W.
CitationJournal: Biochemistry / Year: 2009
Title: Bruno protein contains an expanded RNA recognition motif.
Authors: Lyon, A.M. / Reveal, B.S. / Macdonald, P.M. / Hoffman, D.W.
History
DepositionApr 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Testis-specific RNP-type RNA binding protein


Theoretical massNumber of molelcules
Total (without water)12,2961
Polymers12,2961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Testis-specific RNP-type RNA binding protein


Mass: 12296.016 Da / Num. of mol.: 1 / Fragment: Residues 684-801
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: aret, bruno, CG31762 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: O18409

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the C-terminal RRM3+ of the Bruno protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] 1,0 mM Bruno RRM3+, 1 mM potassium phosphate, 300-400 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1 mM1,0 mM Bruno RRM3+[U-100% 13C; U-100% 15N]1
1 mMpotassium phosphate1
mMsodium chloride300-4001
Sample conditionsIonic strength: 260 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Inova / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: 1.1. / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: simulated annealing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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