[English] 日本語
![](img/lk-miru.gif)
- PDB-3jah: Structure of a mammalian ribosomal termination complex with ABCE1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3jah | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon | ||||||
![]() |
| ||||||
![]() | RIBOSOME / termination / eRF1 / ABCE1 | ||||||
Function / homology | ![]() translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / ribosomal subunit / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / 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 / ribosomal subunit / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cellular response to actinomycin D / ribosomal subunit export from nucleus / cytosolic ribosome / translational termination / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / translational initiation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of ubiquitin-dependent protein catabolic process / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / perikaryon / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / iron ion binding / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
![]() | Brown, A. / Shao, S. / Murray, J. / Hegde, R.S. / Ramakrishnan, V. | ||||||
![]() | ![]() Title: Structural basis for stop codon recognition in eukaryotes. Authors: Alan Brown / Sichen Shao / Jason Murray / Ramanujan S Hegde / V Ramakrishnan / ![]() Abstract: Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal ...Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 5.6 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 366 KB | Display | |
Data in CIF | ![]() | 637.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3039MC ![]() 3038C ![]() 3040C ![]() 3jagC ![]() 3jaiC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
+Protein , 77 types, 77 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein/peptide , 3 types, 3 molecules ln1
#37: Protein/peptide | Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#39: Protein/peptide | Mass: 3213.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#45: Protein/peptide | Mass: 1788.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 7 types, 7 molecules 235789hh
#46: RNA chain | Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#47: RNA chain | Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#48: RNA chain | Mass: 1186579.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#49: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#50: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#51: RNA chain | Mass: 554751.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#85: RNA chain | Mass: 3837.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 207 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ADP.gif)
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | #91: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer solution | Name: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT pH: 7.4 Details: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT | ||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: Quantifoil R2/2 400 mesh Cu grid with thin continuous carbon support, glow discharged | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % Details: After 30 second wait time, blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). Method: After 30 second wait time, blot for 3 seconds before plunging |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Feb 25, 2015 / Details: Automated data acquisition using EPU (FEI) |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1601 |
Radiation wavelength | Relative weight: 1 |
-
Processing
EM software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20515 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||
Refinement step | Cycle: LAST
|