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Yorodumi- PDB-5dmq: Crystal structure of mouse eRF1 in complex with Reverse Transcrip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dmq | ||||||
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Title | Crystal structure of mouse eRF1 in complex with Reverse Transcriptase (RT) of Moloney Murine Leukemia Virus | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/TRANSLATION / complex / eRF1 / RT / HYDROLASE-TRANSLATION complex | ||||||
Function / homology | Function and homology information nucleoside-triphosphatase regulator activity / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / retroviral 3' processing activity / translation termination factor activity / cytoplasmic translational termination / translation release factor complex / host cell late endosome membrane / regulation of translational termination ...nucleoside-triphosphatase regulator activity / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / retroviral 3' processing activity / translation termination factor activity / cytoplasmic translational termination / translation release factor complex / host cell late endosome membrane / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / DNA catabolic process / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / enzyme activator activity / translational termination / cytosolic ribosome / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å | ||||||
Authors | Tang, T. / Song, H. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus Authors: Tang, X. / Zhu, Y. / Baker, S.L. / Bowler, M.W. / Chen, B.J. / Chen, C. / Hogg, J.R. / Goff, S.P. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dmq.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dmq.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dmq ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dmq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 72144.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus (isolate Shinnick) Strain: isolate Shinnick / Production host: Escherichia coli (E. coli) References: UniProt: P03355, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 49092.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BWY3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, 20 % polyacrylic acid sodium salt 5100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4→96.65 Å / Num. obs: 12901 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 4→4.1 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3 |
-Processing
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Refinement | Resolution: 4→96.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 82.814 / SU ML: 1.025 / Cross valid method: THROUGHOUT / ESU R Free: 0.965 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 227.182 Å2
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Refinement step | Cycle: LAST / Resolution: 4→96.65 Å
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