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- PDB-2vxe: SOLUTION STRUCTURE OF THE LSM DOMAIN OF DROSOPHILA MELANOGASTER T... -

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Basic information

Entry
Database: PDB / ID: 2vxe
TitleSOLUTION STRUCTURE OF THE LSM DOMAIN OF DROSOPHILA MELANOGASTER TRAL (TRAILER HITCH)
ComponentsCG10686-PA
KeywordsTRANSCRIPTION / EDC3 / CAR-1 / P-BODIES / DECAPPING / MRNA DECAY / LSM PROTEINS / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


fusome / DEAD/H-box RNA helicase binding / messenger ribonucleoprotein complex / positive regulation of determination of dorsal identity / positive regulation of protein exit from endoplasmic reticulum / P-body assembly / P granule / endoplasmic reticulum organization / stress granule assembly / P-body ...fusome / DEAD/H-box RNA helicase binding / messenger ribonucleoprotein complex / positive regulation of determination of dorsal identity / positive regulation of protein exit from endoplasmic reticulum / P-body assembly / P granule / endoplasmic reticulum organization / stress granule assembly / P-body / microtubule cytoskeleton organization / mRNA processing / actin cytoskeleton organization / mRNA binding / cytosol
Similarity search - Function
FFD box / TFG box / FFD box profile. / TFG box profile. / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain ...FFD box / TFG box / FFD box profile. / TFG box profile. / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / XPLOR
AuthorsTritschler, F. / Coles, M. / Truffault, V.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Similar Modes of Interaction Enable Trailer Hitch and Edc3 to Associate with Dcp1 and Me31B in Distinct Protein Complexes.
Authors: Tritschler, F. / Eulalio, A. / Helms, S. / Schmidt, S. / Coles, M. / Weichenrieder, O. / Izaurralde, E. / Truffault, V.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG10686-PA


Theoretical massNumber of molelcules
Total (without water)9,7771
Polymers9,7771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50MINIMUM ENERGY
RepresentativeModel #1

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Components

#1: Protein CG10686-PA / GH08269P / TRAL-TRAILER HITCH


Mass: 9777.012 Da / Num. of mol.: 1 / Fragment: LSM DOMAIN, RESIDUES 1-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line: S2 CELLS / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / References: UniProt: Q9VTZ0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CO
121HNCO
131HN(CA)CB
141CBCA(CO)NH
151HNHA
161HNHB
171CCH- COSY
181CCH-TOCSY
191HNH-NOESY
1101NNH-NOESY
1111CNH-NOESY
1121HCH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N, AND 13C, 15N-LABELED DROSOPHILA MELANOGASTER TRAL LSM DOMAIN

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Sample preparation

DetailsContents: 1X PBS, 1 MM DTT, PH7.2, 10% D2O
Sample conditionsIonic strength: 150 mM / pH: 7.2 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.4BRUNGERrefinement
SPARKYstructure solution
RefinementMethod: XPLOR / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE PUBLICATION
NMR ensembleConformer selection criteria: MINIMUM ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 24

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