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Yorodumi- PDB-5lzy: Structure of the mammalian rescue complex with Pelota and Hbs1l a... -
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-Basic information
Entry | Database: PDB / ID: 5lzy | ||||||||||||
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Title | Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA. | ||||||||||||
Components |
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Keywords | RIBOSOME / Translation / Elongation | ||||||||||||
Function / homology | Function and homology information stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mesenchymal to epithelial transition / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, non-stop decay / endoderm development / positive regulation of BMP signaling pathway / ribosome disassembly ...stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mesenchymal to epithelial transition / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, non-stop decay / endoderm development / positive regulation of BMP signaling pathway / ribosome disassembly / nonfunctional rRNA decay / regulation of G1 to G0 transition / exit from mitosis / inner cell mass cell proliferation / 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 / optic nerve development / stem cell population maintenance / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / chromosome organization / 90S preribosome / T cell proliferation involved in immune response / translation elongation factor activity / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / ribosome binding / retina development in camera-type eye / 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 / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.99 Å | ||||||||||||
Authors | Shao, S. / Murray, J. / Brown, A. / Taunton, J. / Ramakrishnan, V. / Hegde, R.S. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Cell / Year: 2016 Title: Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Authors: Sichen Shao / Jason Murray / Alan Brown / Jack Taunton / V Ramakrishnan / Ramanujan S Hegde / Abstract: In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the ...In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5lzy.cif.gz | 5.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lzy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5lzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lzy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5lzy_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5lzy_validation.xml.gz | 368.3 KB | Display | |
Data in CIF | 5lzy_validation.cif.gz | 636.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/5lzy ftp://data.pdbj.org/pub/pdb/validation_reports/lz/5lzy | HTTPS FTP |
-Related structure data
Related structure data | 4136MC 4129C 4130C 4131C 4132C 4133C 4134C 4135C 4137C 5lzsC 5lztC 5lzuC 5lzvC 5lzwC 5lzxC 5lzzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 67 types, 67 molecules ABCFGHJLMOPQRSTUVWXYabcdefghjk...
-60S ribosomal protein ... , 4 types, 4 molecules DEZi
#4: Protein | Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6 |
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#5: Protein | Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7 |
#25: Protein | Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6 |
#34: Protein | Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5 |
-Ribosomal protein ... , 3 types, 3 molecules INJJ
#9: Protein | Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2 |
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#13: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1 |
#59: Protein | Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8 |
-Protein/peptide , 1 types, 1 molecules n
#39: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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-RNA chain , 6 types, 7 molecules 235789hh
#45: RNA chain | Mass: 24102.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #46: RNA chain | | Mass: 1148115.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #47: RNA chain | | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #48: RNA chain | | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #49: RNA chain | | Mass: 602778.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #83: RNA chain | | Mass: 2588.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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-40S ribosomal protein ... , 4 types, 4 molecules BBGGMMbb
#51: Protein | Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70 |
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#56: Protein | Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55 |
#62: Protein | Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8 |
#77: Protein | Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76 |
-Non-polymers , 3 types, 245 molecules
#86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-ZN / #88: Chemical | ChemComp-GCP / | |
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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: Affinity-purified 80S ribosome-nascent chain complex reconstituted with Pelota and Hbs1l. Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 3.3 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: 3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1112 |
Image scans | Movie frames/image: 16 |
-Processing
Software | Name: REFMAC / Version: 5.8.0124 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 138488 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20717 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 63.6 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSCaverage | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.99→300.16 Å / Cor.coef. Fo:Fc: 0.911 / SU B: 44.594 / SU ML: 0.598 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.818 Å2
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Refinement step | Cycle: 1 / Total: 221906 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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