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- PDB-4a53: Structural basis of the Dcp1:Dcp2 mRNA decapping complex activati... -

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Basic information

Entry
Database: PDB / ID: 4a53
TitleStructural basis of the Dcp1:Dcp2 mRNA decapping complex activation by Edc3 and Scd6
ComponentsEDC3
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / P-body assembly / P-body / cytoplasmic stress granule / mRNA binding / cytoplasm
Similarity search - Function
Lsm16, N-terminal / FDF domain / FDF domain / FDF / DFDF domain / DFDF domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain superfamily / YjeF N-terminal domain / YjeF N-terminal domain profile. ...Lsm16, N-terminal / FDF domain / FDF domain / FDF / DFDF domain / DFDF domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain superfamily / YjeF N-terminal domain / YjeF N-terminal domain profile. / SH3 type barrels. - #100 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodSOLUTION NMR / XPLOR
AuthorsFromm, S.A. / Truffault, V. / Kamenz, J. / Braun, J.E. / Hoffmann, N.A. / Izaurralde, E. / Sprangers, R.
CitationJournal: Embo J. / Year: 2011
Title: The Structural Basis of Edc3- and Scd6-Mediated Activation of the Dcp1:Dcp2 Mrna Decapping Complex.
Authors: Fromm, S.A. / Truffault, V. / Kamenz, J. / Braun, J.E. / Hoffmann, N.A. / Izaurralde, E. / Sprangers, R.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EDC3


Theoretical massNumber of molelcules
Total (without water)14,0171
Polymers14,0171
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)20 / 50LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein EDC3 / / UNCHARACTERIZED PROTEIN C18E5.11C


Mass: 14016.722 Da / Num. of mol.: 1 / Fragment: LSM, RESIDUES 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O94752

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 125 mM / pH: 7.3 / Pressure: 1.0 atm / Temperature: 303.0 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
X-PLOR2.9.3SCHWIETERS CDrefinement
SPARKYstructure solution
RefinementMethod: XPLOR / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 20

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