+Open data
-Basic information
Entry | Database: PDB / ID: 4crm | ||||||
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Title | Cryo-EM of a pre-recycling complex with eRF1 and ABCE1 | ||||||
Components |
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Keywords | TRANSLATION / TERMINATION / RECYCLING | ||||||
Function / homology | Function and homology information Eukaryotic Translation Termination / sno(s)RNA transcription / cytoplasmic translational termination / translation release factor complex / translation release factor activity / translation release factor activity, codon specific / ribosome disassembly / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Eukaryotic Translation Termination / sno(s)RNA transcription / cytoplasmic translational termination / translation release factor complex / translation release factor activity / translation release factor activity, codon specific / ribosome disassembly / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit binding / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / ribosomal large subunit biogenesis / positive regulation of translation / translational initiation / DNA-templated transcription termination / cytoplasmic stress granule / rRNA processing / iron ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.75 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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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4crm.cif.gz | 171.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crm.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 4crm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4crm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4crm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4crm_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 4crm_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crm ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crm | HTTPS FTP |
-Related structure data
Related structure data | 2598MC 2597C 4crnC 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
-Protein , 2 types, 2 molecules PX
#1: Protein | Mass: 68433.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PYES2 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q03195 |
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#2: Protein | Mass: 31355.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12385 |
-Non-polymers , 5 types, 6 molecules
#3: Chemical | ChemComp-ATP / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE FIRST 139 AMINO ACIDS ARE MISSING. THE C-TERMINAL AMINO ACIDS 422-440 ARE MISSING |
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-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 | Name: 20 MM HEPES PH 7.5, 200 MM KCL, 1.5 MGCL2, 2 MM DTT, 0.01 MG/ML CYCLOHEXIMIDE, 0.05 % NIKKOL, 0.03 % DBC, 0.5 MM ADPNP). pH: 7.5 Details: 20 MM HEPES PH 7.5, 200 MM KCL, 1.5 MGCL2, 2 MM DTT, 0.01 MG/ML CYCLOHEXIMIDE, 0.05 % NIKKOL, 0.03 % DBC, 0.5 MM ADPNP). |
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: VITRIFICATION 1 -CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING |
-Electron microscopy imaging
Microscopy | Model: FEI MORGAGNI / Date: Feb 20, 2013 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 147136 X / Cs: 2.7 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: ON VOLUMES (SPIDER) | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 8.75 Å / Num. of particles: 39309 / Actual pixel size: 1.0605 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2598. Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY | ||||||||||||||||||
Atomic model building | PDB-ID: 1DT9 Accession code: 1DT9 / Source name: PDB / Type: experimental model | ||||||||||||||||||
Refinement | Highest resolution: 8.75 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.75 Å
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