[English] 日本語
Yorodumi- PDB-3j5y: Structure of the mammalian ribosomal pre-termination complex asso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j5y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the mammalian ribosomal pre-termination complex associated with eRF1-eRF3-GDPNP | |||||||||
Components |
| |||||||||
Keywords | TRANSLATION/RNA / Translation termination / eRF1 / eRF3 / tRNAleu / ribosome / mammalian / TRANSLATION-RNA complex | |||||||||
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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / ribosome binding / translation / GTPase activity / GTP binding / RNA binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.7 Å | |||||||||
Authors | des Georges, A. / Hashem, Y. / Unbehaun, A. / Grassucci, R.A. / Taylor, D. / Hellen, C.U.T. / Pestova, T.V. / Frank, J. | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2014 Title: Structure of the mammalian ribosomal pre-termination complex associated with eRF1.eRF3.GDPNP. Authors: Amédée des Georges / Yaser Hashem / Anett Unbehaun / Robert A Grassucci / Derek Taylor / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Abstract: Eukaryotic translation termination results from the complex functional interplay between two release factors, eRF1 and eRF3, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl- ...Eukaryotic translation termination results from the complex functional interplay between two release factors, eRF1 and eRF3, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, we present a cryo-electron microscopy structure of pre-termination complexes associated with eRF1•eRF3•GDPNP at 9.7 -Å resolution, which corresponds to the initial pre-GTP hydrolysis stage of factor attachment and stop codon recognition. It reveals the ribosomal positions of eRFs and provides insights into the mechanisms of stop codon recognition and triggering of eRF3's GTPase activity. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j5y.cif.gz | 210 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3j5y.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 3j5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j5y_validation.pdf.gz | 816.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3j5y_full_validation.pdf.gz | 929.8 KB | Display | |
Data in XML | 3j5y_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 3j5y_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5y ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5y | HTTPS FTP |
-Related structure data
Related structure data | 5801MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 46478.121 Da / Num. of mol.: 1 / Fragment: UNP residues 7-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62495 |
---|---|
#2: Protein | Mass: 48030.508 Da / Num. of mol.: 1 / Fragment: UNP residues 69-496 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSPT1, ERF3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P15170 |
#3: RNA chain | Mass: 3193.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: messenger RNA / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#4: RNA chain | Mass: 28376.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 4.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Buffer solution | Name: 20 mM Tris, 100 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine supplemented with 200 units RNasin, 0.4 mM ATP, 3 mM Mg-GMPPNP pH: 7.5 Details: 20 mM Tris, 100 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine supplemented with 200 units RNasin, 0.4 mM ATP, 3 mM Mg-GMPPNP | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Details: Quantifoil grids, glow discharged | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 93 K / Humidity: 100 % / Details: plunged into liquid ethane (FEI VITROBOT MARK IV) |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI POLARA 300 / Date: Jan 1, 2010 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.1 mm |
Specimen holder | Specimen holder model: GATAN HELIUM / Temperature: 81 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: Each Particle | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Method: reference-based reconstruction / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48973 Details: (Single particle details: Images were classified and refined with RELION) (Single particle--Applied symmetry: C1) Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST
|