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Yorodumi- PDB-5k0y: m48S late-stage initiation complex, purified from rabbit reticulo... -
+Open data
-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 2 complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition ...viral translational termination-reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / 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 / phagocytic cup / ubiquitin ligase inhibitor activity / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / T cell proliferation involved in immune response / regulation of translational fidelity / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / 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) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / modification-dependent protein catabolic process / spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / virus receptor activity / ribosome binding / 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 / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / GTPase activity / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / negative regulation of apoptotic process / nucleolus / GTP binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding 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 |