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Yorodumi- PDB-2lyd: The solution structure of the Dm DCP1 EVH1 domain in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lyd | ||||||
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Title | The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide | ||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING / DCP1 / XRN1 / TRANSCRIPTION-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information : / regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / positive regulation of imaginal disc growth / imaginal disc fusion, thorax closure / mRNA decay by 5' to 3' exoribonuclease / regulation of cytoplasmic mRNA processing body assembly / pole plasm / dorsal closure / pole plasm oskar mRNA localization / : ...: / regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / positive regulation of imaginal disc growth / imaginal disc fusion, thorax closure / mRNA decay by 5' to 3' exoribonuclease / regulation of cytoplasmic mRNA processing body assembly / pole plasm / dorsal closure / pole plasm oskar mRNA localization / : / deadenylation-independent decapping of nuclear-transcribed mRNA / neuronal ribonucleoprotein granule / imaginal disc-derived wing morphogenesis / positive regulation of mRNA catabolic process / 5'-3' RNA exonuclease activity / nuclear-transcribed mRNA catabolic process, non-stop decay / deadenylation-dependent decapping of nuclear-transcribed mRNA / rRNA catabolic process / miRNA-mediated post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / P granule / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / 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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Truffault, V. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lyd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lyd.ent.gz | 949.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lyd_validation.pdf.gz | 409.3 KB | Display | wwPDB validaton report |
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Full document | 2lyd_full_validation.pdf.gz | 603.9 KB | Display | |
Data in XML | 2lyd_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 2lyd_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/2lyd ftp://data.pdbj.org/pub/pdb/validation_reports/ly/2lyd | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein/peptide | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 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 | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 300 / pH: 7.1 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR constraints | NOE 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 representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 21 |