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Yorodumi- EMDB-5801: Structure of the mammalian ribosomal pre-termination complex asso... -
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-Basic information
Entry | Database: EMDB / ID: EMD-5801 | ||||||||||||
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Title | Structure of the mammalian ribosomal pre-termination complex associated with eRF1-eRF3-GDPNP | ||||||||||||
Map data | Reconstruction of the eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex assembled in vitro on a derivative of beta-globin mRNA encoding MVHL tetrapeptide followed by a UAA stop codon. The P-site is occupied by a tRNAleu. | ||||||||||||
Sample |
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Keywords | Translation termination / eRF1 / eRF3 / tRNAleu / ribosome / mammalian | ||||||||||||
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 / Regulation of expression of SLITs and ROBOs / G1/S transition of mitotic cell cycle / ribosome binding / translation / GTPase activity / GTP binding / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.7 Å | ||||||||||||
Authors | des Georges A / Hashem H / Unbehaun A / Grassucci RA / Taylor D / Hellen CUT / Pestova TV / 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5801.map.gz | 101.4 MB | EMDB map data format | |
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Header (meta data) | emd-5801-v30.xml emd-5801.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_5801_fsc.xml emd_5801_fsc_1.xml | 12.6 KB 12.7 KB | Display Display | FSC data file |
Images | emd_5801.jpg | 48.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5801 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5801 | HTTPS FTP |
-Validation report
Summary document | emd_5801_validation.pdf.gz | 374.2 KB | Display | EMDB validaton report |
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Full document | emd_5801_full_validation.pdf.gz | 373.8 KB | Display | |
Data in XML | emd_5801_validation.xml.gz | 11.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5801 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5801 | HTTPS FTP |
-Related structure data
Related structure data | 3j5yMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5801.map.gz / Format: CCP4 / Size: 104.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex assembled in vitro on a derivative of beta-globin mRNA encoding MVHL tetrapeptide followed by a UAA stop codon. The P-site is occupied by a tRNAleu. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex
Entire | Name: eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex |
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Components |
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-Supramolecule #1000: eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex
Supramolecule | Name: eRF1-eRF3-GDPNP-bound mammalian ribosomal pre-termination complex type: sample / ID: 1000 / Number unique components: 5 |
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Molecular weight | Theoretical: 4.5 MDa / Method: calculation |
-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: blood / Cell: red blood cells |
Molecular weight | Theoretical: 4.5 MDa |
-Macromolecule #1: eukaryotic release factor 1
Macromolecule | Name: eukaryotic release factor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: eRF1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Molecular weight | Theoretical: 480 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Eukaryotic peptide chain release factor subunit 1 |
-Macromolecule #2: eukaryotic release factor 3
Macromolecule | Name: eukaryotic release factor 3 / type: protein_or_peptide / ID: 2 / Name.synonym: eRF3 / Details: 138 aa N-terminal deletion / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Molecular weight | Theoretical: 540 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A |
-Macromolecule #3: Transfer-messenger RNA Leu
Macromolecule | Name: Transfer-messenger RNA Leu / type: rna / ID: 3 / Name.synonym: tRNAleu Details: Native tRNAs were aminoacylated with Met, Val, His, and Leu using native aminoacyl-tRNA synthetases. Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit |
Molecular weight | Theoretical: 25 KDa |
-Macromolecule #4: messenger RNA
Macromolecule | Name: messenger RNA / type: rna / ID: 4 / Name.synonym: mRNA Details: beta-globin mRNA encoding MVHL tetrapeptide followed by a UAA stop codon Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | 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 |
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Staining | Type: NEGATIVE / Details: cryo |
Grid | Details: Quantifoil grids, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 1, 2010 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: F |
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Software | Name: Chimera |
Details | Domains were fitted as rigid bodies using Chimera. Individual domains were then refined manually using hinge points as points of flexibility. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |
Output model | PDB-3j5y: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |
Output model | PDB-3j5y: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |
Output model | PDB-3j5y: |
-Atomic model buiding 4
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation |
Output model | PDB-3j5y: |