+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3099 | |||||||||
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Title | Cryo-EM structure of a human translation termination complex | |||||||||
Map data | Cryo-EM structure of a human translation termination complex | |||||||||
Sample |
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Keywords | human / 80S / ribosome / eRF1 / translation termination / CMV / stalling | |||||||||
Function / homology | Function and homology information translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / 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 / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / 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 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / translational termination / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / large ribosomal subunit rRNA binding / ribosome binding / cytoplasmic translation / cytosolic large ribosomal subunit / postsynaptic density / structural constituent of ribosome / translation / ribonucleoprotein complex / focal adhesion / nucleolus / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Matheisl S / Berninghausen O / Becker T / Beckmann R | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2015 Title: Structure of a human translation termination complex. Authors: Sarah Matheisl / Otto Berninghausen / Thomas Becker / Roland Beckmann / Abstract: In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the ...In contrast to bacteria that have two release factors, RF1 and RF2, eukaryotes only possess one unrelated release factor eRF1, which recognizes all three stop codons of the mRNA and hydrolyses the peptidyl-tRNA bond. While the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. Here we present a 3.8 Å structure of a human translation termination complex with eRF1 decoding a UAA(A) stop codon. The complex was formed using the human cytomegalovirus (hCMV) stalling peptide, which perturbs the peptidyltransferase center (PTC) to silence the hydrolysis activity of eRF1. Moreover, unlike sense codons or bacterial stop codons, the UAA stop codon adopts a U-turn-like conformation within a pocket formed by eRF1 and the ribosome. Inducing the U-turn conformation for stop codon recognition rationalizes how decoding by eRF1 includes monitoring geometry in order to discriminate against sense codons. | |||||||||
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_3099.map.gz | 263 MB | EMDB map data format | |
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Header (meta data) | emd-3099-v30.xml emd-3099.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_3099.png | 587.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3099 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3099 | HTTPS FTP |
-Related structure data
Related structure data | 5a8lMC 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_3099.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of a human translation termination complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.062 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 : CMV stalled human 80S ribosome bound to the translation terminati...
Entire | Name: CMV stalled human 80S ribosome bound to the translation termination factor eRF1 |
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Components |
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-Supramolecule #1000: CMV stalled human 80S ribosome bound to the translation terminati...
Supramolecule | Name: CMV stalled human 80S ribosome bound to the translation termination factor eRF1 type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 4.5 MDa / Theoretical: 4.5 MDa / Method: Sedimentation |
-Supramolecule #1: Human 80S ribosome
Supramolecule | Name: Human 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa S3 spinner cells |
Molecular weight | Experimental: 4.5 MDa / Theoretical: 4.5 MDa |
-Macromolecule #1: translation termination factor eRF1
Macromolecule | Name: translation termination factor eRF1 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: HUMAN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 20 mM HEPES, 100 mM KOAc, 2.5 mM Mg(OAc)2, 0.25 mM spermidine, 2 mM DTT, 0.06 U/uL RNasin (Ambion), 1/625 EDTA-free complete protease inhibitor (Roche) |
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Grid | Details: 2 nm pre-coated Quantifoil R3/3 holey carbon supported grids |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Mar 11, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). Number images used: 33165 |