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Yorodumi- PDB-1dt9: THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MEC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dt9 | ||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MECHANISM OF STOP CODON RECOGNITION AND PEPTIDYL-TRNA HYDROLYSIS | ||||||
Components | PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1) | ||||||
Keywords | TRANSLATION / erf1 / trna mimicry / protein sythesis / stop codon recognition / peptidyl-trna hydrolysis | ||||||
Function / homology | Function and homology information translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / 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) / translational termination / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / ribosome binding / RNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Frolova, L. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Authors: Song, H. / Mugnier, P. / Das, A.K. / Webb, H.M. / Evans, D.R. / Tuite, M.F. / Hemmings, B.A. / Barford, D. #1: Journal: RNA / Year: 1999 Title: Mutations in the Highly Conserved GGQ Motif of Class 1 Polypeptide Release Factors Abolish Ability of Human eRF1 to Trigger Peptidyl-tRNA Hydrolysis. Authors: Frolova, L.Y. / Tsivkovskii, R.Y. / Sivolobova, G.F. / Oparina, N.Y. / Serpinsky, O.I. / Blinov, V.M. / Tatkov, S.I. / Kisselev, L.L. #2: Journal: Nature / Year: 1994 Title: A Highly Conserved Eukaryotic Protein Family Possesing Properties of Polypeptide Chain Release Factor Authors: Frolova, L. / Le Goff, X. / Rasmussen, H.H. / Cheperegin, S. / Drugeon, G. / Kress, M. / Arman, I. / Haenni, A.L. / Celis, J.E. / Philippe, M. / Justesen, J. / Kisselev, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dt9.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dt9.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dt9_validation.pdf.gz | 416.1 KB | Display | wwPDB validaton report |
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Full document | 1dt9_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 1dt9_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 1dt9_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dt9 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dt9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49092.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62495 |
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#2: 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: 2.94 Å3/Da / Density % sol: 58.17 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes, PEG4000, Glycerol, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: protein was mixed with equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A |
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Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 82505 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.7→25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.406 / Num. unique all: 16712 / % possible all: 98 |
Reflection | *PLUS Num. obs: 16712 / Num. measured all: 82505 |
Reflection shell | *PLUS % possible obs: 98 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.7→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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