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- PDB-4a54: Structural basis of the Dcp1:Dcp2 mRNA decapping complex activati... -

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Basic information

Entry
Database: PDB / ID: 4a54
TitleStructural basis of the Dcp1:Dcp2 mRNA decapping complex activation by Edc3 and Scd6
Components
  • EDC3
  • MRNA DECAPPING COMPLEX SUBUNIT 2
KeywordsRNA BINDING PROTEIN/HYDROLASE / RNA BINDING PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / P-body / molecular condensate scaffold activity / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / mRNA binding / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Lsm16, N-terminal / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. ...Lsm16, N-terminal / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / SH3 type barrels. - #100 / : / Sm domain profile. / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
mRNA decapping complex subunit 2 / 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
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EDC3
B: MRNA DECAPPING COMPLEX SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)15,9452
Polymers15,9452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 50LOWEST ENERGY
RepresentativeModel #1

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Components

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


Mass: 10601.993 Da / Num. of mol.: 1 / Fragment: LSM, RESIDUES 1-94
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
#2: Protein MRNA DECAPPING COMPLEX SUBUNIT 2 / DCP2


Mass: 5342.786 Da / Num. of mol.: 1 / Fragment: HLM1, RESIDUES 242-291
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: O13828, Hydrolases

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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: 22

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