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Yorodumi- PDB-5k0y: m48S late-stage initiation complex, purified from rabbit reticulo... -
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-Basic information
Entry | Database: PDB / ID: 5k0y | |||||||||
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Title | m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face | |||||||||
Components |
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Keywords | TRANSLATION / eukaryotic translation initiation / ribosome / eIF3 peripheral subunits / cryo-EM | |||||||||
Function / homology | Function and homology information viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / phagocytic cup / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / laminin binding / 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 / cytosolic ribosome / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / spindle / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / cytoplasmic translation / perikaryon / cytosolic large ribosomal subunit / tRNA binding / mitochondrial inner membrane / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / cell division / DNA repair / GTPase activity / mRNA binding / centrosome / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / negative regulation of apoptotic process / nucleolus / GTP binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Simonetti, A. / Brito Querido, J. / Myasnikov, A.G. / Mancera-Martinez, E. / Renaud, A. / Kuhn, L. / Hashem, Y. | |||||||||
Funding support | France, 2items
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Citation | Journal: Mol Cell / Year: 2016 Title: eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Authors: Angelita Simonetti / Jailson Brito Querido / Alexander G Myasnikov / Eder Mancera-Martinez / Adeline Renaud / Lauriane Kuhn / Yaser Hashem / Abstract: mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal ...mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining. | |||||||||
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 | 5k0y.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5k0y.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 5k0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k0y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5k0y_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5k0y_validation.xml.gz | 203.7 KB | Display | |
Data in CIF | 5k0y_validation.cif.gz | 340.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/5k0y ftp://data.pdbj.org/pub/pdb/validation_reports/k0/5k0y | HTTPS FTP |
-Related structure data
Related structure data | 8190MC 8195C 5k1hC 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
-RNA chain , 3 types, 3 molecules NAF
#1: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNAiMet / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: REF: 655840029 |
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#2: RNA chain | Mass: 572789.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: REF: 283837872 |
#3: RNA chain | Mass: 9603.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Beta-Globin mRNA / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) |
-Protein , 1 types, 1 molecules P
#4: Protein | Mass: 30633.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: EIF2S1 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4 |
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+Ribosomal protein ... , 26 types, 26 molecules GHJKLQRUVWXZacefghijklmnpt
-40S ribosomal protein ... , 7 types, 7 molecules IYboqrs
#7: Protein | Mass: 29658.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS4X / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17 |
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#21: Protein | Mass: 9480.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS27 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76 |
#24: Protein | Mass: 8896.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS21 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82 |
#37: Protein | Mass: 23902.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS8 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1 |
#39: Protein | Mass: 27471.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100339133, RPS6 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55 |
#40: Protein | Mass: 13766.122 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS12 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8 |
#41: Protein | Mass: 15188.970 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS24 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40 |
-Eukaryotic translation initiation factor 3 subunit ... , 3 types, 3 molecules MOT
#11: Protein/peptide | Mass: 4124.495 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3G, EIF3S4 / Production host: Homo sapiens (human) / References: UniProt: O75821 |
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#12: Protein | Mass: 8675.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3G, EIF3S4 / Production host: Homo sapiens (human) / References: UniProt: O75821 |
#16: Protein | Mass: 37039.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: EIF3I, EIF3S2 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: Q5IH81 |
-Eukaryotic initiation factor 2 ... , 2 types, 2 molecules Sd
#15: Protein | Mass: 45862.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SRA8*PLUS |
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#26: Protein/peptide | Mass: 2103.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: Q97W59*PLUS |
-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: m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2 MDa / Experimental value: NO |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 0.5 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 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal defocus max: 4500 nm / Nominal defocus min: 800 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 24 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5700 |
Image scans | Sampling size: 14 µm / Movie frames/image: 7 / Used frames/image: 2-8 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 475000 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4KZY |