[English] 日本語
![](img/lk-miru.gif)
- EMDB-2598: Cryo-EM of a termination/pre-recycling complex with eRF1 and ABCE1 -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-2598 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM of a termination/pre-recycling complex with eRF1 and ABCE1 | |||||||||
![]() | "CMV-stalled" wheat germ 80S-RNC bound to eRF1 and ABCE1. | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() Eukaryotic Translation Termination / translation release factor complex / cytoplasmic translational termination / translation release factor activity / translation release factor activity, codon specific / ribosome disassembly / sequence-specific mRNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Preis A / Heuer A / Barrio-Garcia C / Hauser A / Eyler D / Berninghausen O / Green R / Becker T / Beckmann R | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 24.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 12.1 KB 12.1 KB | Display Display | ![]() |
Images | ![]() | 268.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4crmMC ![]() 2597C ![]() 4crnC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | "CMV-stalled" wheat germ 80S-RNC bound to eRF1 and ABCE1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
Entire | Name: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP |
---|---|
Components |
|
-Supramolecule #1000: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
Supramolecule | Name: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP type: sample / ID: 1000 Oligomeric state: One ribosome binds to one eRF1 and one ABCE1 Number unique components: 3 |
---|
-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Sup45
Macromolecule | Name: Sup45 / type: protein_or_peptide / ID: 1 / Name.synonym: eRF1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 49 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #2: Rli1
Macromolecule | Name: Rli1 / type: protein_or_peptide / ID: 2 / Name.synonym: ABCE1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 68 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | 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). |
---|---|
Staining | Type: NEGATIVE / Details: Cryo-EM |
Grid | Details: Sec61 was added at a five-fold molar excess to saturate the hydrophobic signal-anchor sequence and avoid orientational bias on the cryo-grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 147136 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Feb 20, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
CTF correction | Details: on volumes (SPIDER) |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.75 Å / Resolution method: OTHER / Software - Name: StarFish, SPIDER / Details: Data-subset resulted from computational sorting / Number images used: 39309 |
Details | The particles were picked with starfish_boxing version 0.2.0, which is part of the new StarFish single particle analysis program suite. |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: Chimera, Coot, MDFF |
Details | A homology model of eRF1 was created using HHPred. The domains were separately fitted by manual docking using program Coot. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-4crm: |