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- PDB-2lyd: The solution structure of the Dm DCP1 EVH1 domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 2lyd
TitleThe solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide
Components
  • Decapping protein 1
  • Pacman protein
KeywordsTRANSCRIPTION/PROTEIN BINDING / DCP1 / XRN1 / TRANSCRIPTION-PROTEIN BINDING complex
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / imaginal disc fusion, thorax closure / positive regulation of imaginal disc growth / mRNA decay by 5' to 3' exoribonuclease / RNA-mediated post-transcriptional gene silencing => GO:0035194 / regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / pole plasm / dorsal closure ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / imaginal disc fusion, thorax closure / positive regulation of imaginal disc growth / mRNA decay by 5' to 3' exoribonuclease / RNA-mediated post-transcriptional gene silencing => GO:0035194 / regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / pole plasm / dorsal closure / pole plasm oskar mRNA localization / deadenylation-independent decapping of nuclear-transcribed mRNA / neuronal ribonucleoprotein granule / imaginal disc-derived wing morphogenesis / miRNA-mediated gene silencing / 5'-3' exoribonuclease activity / nuclear-transcribed mRNA catabolic process, non-stop decay / messenger ribonucleoprotein complex / RNA-mediated post-transcriptional gene silencing / rRNA catabolic process / deadenylation-dependent decapping of nuclear-transcribed mRNA / P granule / nuclear-transcribed mRNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA catabolic process / positive regulation of catalytic activity / enzyme activator activity / P-body / wound healing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / spermatogenesis / negative regulation of gene expression / mRNA binding / neuronal cell body / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
5-3 exonuclease XRN1, DCP1-binding motif / 5-3 exonuclease XRN1 DCP1-binding motif / mRNA-decapping enzyme C-terminus / mRNA-decapping enzyme, C-terminal / Exoribonuclease Xrn1, D2/D3 domain / 5'-3' exoribonuclease 1, SH3-like domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, D1 domain / Xrn1 SH3-like domain / Exoribonuclease Xrn1 D1 domain ...5-3 exonuclease XRN1, DCP1-binding motif / 5-3 exonuclease XRN1 DCP1-binding motif / mRNA-decapping enzyme C-terminus / mRNA-decapping enzyme, C-terminal / Exoribonuclease Xrn1, D2/D3 domain / 5'-3' exoribonuclease 1, SH3-like domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, D1 domain / Xrn1 SH3-like domain / Exoribonuclease Xrn1 D1 domain / 5'-3' exoribonuclease 1 / 5'-3' exoribonuclease / Xrn1 helical domain / Xrn1, N-terminal / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Dcp1-like decapping family / mRNA-decapping enzyme subunit 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
5'-3' exoribonuclease 1 / Decapping protein 1, isoform A / 5'-3' exoribonuclease 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsTruffault, V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation.
Authors: Braun, J.E. / Truffault, V. / Boland, A. / Huntzinger, E. / Chang, C.T. / Haas, G. / Weichenrieder, O. / Coles, M. / Izaurralde, E.
History
DepositionSep 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 19, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decapping protein 1
B: Pacman protein


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
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)21 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Decapping protein 1 /


Mass: 15474.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dcp1, CG11183, Dmel_CG11183 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9W1H5
#2: Protein/peptide Pacman protein


Mass: 4355.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pcm, pacman, CG3291 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XZU2, UniProt: E1JJR3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D C(CO)NH
1313D HN(CA)CB
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNHA
1713D (H)CCH-TOCSY
1813D HNHB
1912D NOESYnoN
11012D PLUSH-TACSY
11113D NNH NOESY
11213D CNH NOESY
11313D CCH NOESY
11414D CCANH

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Sample preparation

DetailsContents: 0.4 mM [U-100% 15N] protein_1, 0.7 mM [U-100% 13C; U-100% 15N] protein_1, 0.4 mM [U-100% 15N] protein_2, 0.7 mM [U-100% 13C; U-100% 15N] protein_2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity_1-1[U-100% 15N]1
0.7 mMentity_1-2[U-100% 13C; U-100% 15N]1
0.4 mMentity_2-3[U-100% 15N]1
0.7 mMentity_2-4[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 300 / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameDeveloperClassification
SPARKYGoddardchemical shift assignment
XPLORBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 690 / NOE intraresidue total count: 131 / NOE long range total count: 210 / NOE medium range total count: 52 / NOE sequential total count: 268
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21

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