+Open data
-Basic information
Entry | Database: PDB / ID: 4crn | ||||||
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Title | Cryo-EM of a pretermination complex with eRF1 and eRF3 | ||||||
Components |
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Keywords | TRANSLATION / TERMINATION / CRYO-EM | ||||||
Function / homology | Function and homology information Eukaryotic Translation Termination / translation release factor complex / cytoplasmic translational termination / translation release factor activity / translation release factor activity, codon specific / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...Eukaryotic Translation Termination / translation release factor complex / cytoplasmic translational termination / translation release factor activity / translation release factor activity, codon specific / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / translation / GTPase activity / mRNA binding / GTP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.1 Å | ||||||
Authors | Preis, A. / Heuer, A. / Barrio-Garcia, C. / Hauser, A. / Eyler, D. / Berninghausen, O. / Green, R. / Becker, T. / Beckmann, R. | ||||||
Citation | Journal: Cell Rep / Year: 2014 Title: Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. Authors: Anne Preis / Andre Heuer / Clara Barrio-Garcia / Andreas Hauser / Daniel E Eyler / Otto Berninghausen / Rachel Green / Thomas Becker / Roland Beckmann / Abstract: Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and ...Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and guanosine triphosphate (GTP)-bound eRF3. After GTP hydrolysis, eRF3 dissociates, and ABCE1 can bind to eRF1-loaded ribosomes to stimulate peptide release and ribosomal subunit dissociation. Here, we present cryoelectron microscopic (cryo-EM) structures of a pretermination complex containing eRF1-eRF3 and a termination/prerecycling complex containing eRF1-ABCE1. eRF1 undergoes drastic conformational changes: its central domain harboring the catalytically important GGQ loop is either packed against eRF3 or swung toward the peptidyl transferase center when bound to ABCE1. Additionally, in complex with eRF3, the N-terminal domain of eRF1 positions the conserved NIKS motif proximal to the stop codon, supporting its suggested role in decoding, yet it appears to be delocalized in the presence of ABCE1. These results suggest that stop codon decoding and peptide release can be uncoupled during termination. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4crn.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crn.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 4crn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4crn_validation.pdf.gz | 906.8 KB | Display | wwPDB validaton report |
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Full document | 4crn_full_validation.pdf.gz | 1015.8 KB | Display | |
Data in XML | 4crn_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 4crn_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crn ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crn | HTTPS FTP |
-Related structure data
Related structure data | 2597MC 2598C 4crmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 47840.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FOR CHAIN P (ERF3) THE FIRST 254 AMINO ACIDS ARE MISSING. Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTYB2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05453 |
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#2: Protein | Mass: 49032.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FOR CHAIN X THE LAST 25 AMINO ACIDS (416-440) ARE MISSING Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTYB2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12385 |
#3: Chemical | ChemComp-GNP / |
Sequence details | THE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS ...THE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS (RESIDUES 416-440) ARE MISSING IN THE MODEL |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CMV-STALLED WHEAT GERM 80S-RNC BOUND TO ERF1 AND ABCE1-ADPNP Type: RIBOSOME |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE, VITROBOT MARK 4 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Feb 20, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 147136 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm |
Image recording | Electron dose: 0.02 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 9.1 Å / Num. of particles: 39309 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2597 (DEPOSITION ID: 12368). Symmetry type: POINT | |||||||||||||||
Refinement | Highest resolution: 9.1 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.1 Å
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