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Yorodumi- PDB-5dmr: Crystal Structure of C-terminal domain of mouse eRF1 in complex w... -
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-Basic information
Entry | Database: PDB / ID: 5dmr | ||||||
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Title | Crystal Structure of C-terminal domain of mouse eRF1 in complex with RNase H domain of RT of Moloney Murine Leukemia Virus | ||||||
Components |
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Keywords | HYDROLASE/TRANSLATION / eRF1 / RT / complex / 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 / translation release factor complex / cytoplasmic translational termination / host cell late endosome membrane / translation release factor activity ...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 / translation release factor complex / cytoplasmic translational termination / host cell late endosome membrane / translation release factor activity / regulation of translational termination / 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 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / translational termination / cytosolic ribosome / enzyme activator activity / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tang, X. / 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 | 5dmr.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dmr.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dmr_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 5dmr_full_validation.pdf.gz | 444.5 KB | Display | |
Data in XML | 5dmr_validation.xml.gz | 11 KB | Display | |
Data in CIF | 5dmr_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dmr ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dmr | HTTPS FTP |
-Related structure data
Related structure data | 5dmqC 1dt9S 2hb5S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 18766.250 Da / Num. of mol.: 1 / Fragment: RNase H domain, UNP residues 1159-1330 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, ribonuclease H |
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#2: Protein | Mass: 18777.975 Da / Num. of mol.: 1 / Fragment: C-terminal residues 276-437 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 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 18 % ammonium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. obs: 8469 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HB5 and 1DT9 Resolution: 2.8→59.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.158 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / 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: 75.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→59.99 Å
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