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- PDB-3jap: Structure of a partial yeast 48S preinitiation complex in closed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jap | ||||||
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Title | Structure of a partial yeast 48S preinitiation complex in closed conformation | ||||||
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![]() | TRANSLATION / Eukaryotic translation initiation / 48S / small ribosome subunit / 40S / 43S | ||||||
Function / homology | ![]() formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site ...formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site / multi-eIF complex / eukaryotic translation initiation factor 3 complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / 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) / translation initiation factor binding / translational initiation / translation initiation factor activity / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / double-stranded RNA binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||
![]() | Llacer, J.L. / Hussain, T. / Ramakrishnan, V. | ||||||
![]() | ![]() Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan / ![]() ![]() Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 192 KB | Display | |
Data in CIF | ![]() | 332.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3048MC ![]() 3047C ![]() 3049C ![]() 3050C ![]() 3jamC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules 123
#1: RNA chain | Mass: 24223.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: RNA chain | Mass: 573814.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 7786.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
+Protein , 42 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-Protein/peptide , 2 types, 2 molecules hr
#37: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#46: Protein/peptide | Mass: 3963.560 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
-Non-polymers , 4 types, 87 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/GCP.gif)
#48: Chemical | ChemComp-MG / #49: Chemical | ChemComp-ZN / #50: Chemical | ChemComp-MET / | #51: 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 |
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Sample preparation
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Buffer solution | Name: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT pH: 6.5 Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Details: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 % Details: Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I). Method: Blot for 2.5 to 3 seconds before plunging |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 4, 2014 Details: Complete dataset was collected over two non-consecutive days. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder type: GATAN LIQUID NITROGEN |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 5500 |
Radiation wavelength | Relative weight: 1 |
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Processing
Software | Name: REFMAC / Version: 5.8.0124 2015/06/03 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk Description: (un)restrained refinement or idealisation of macromolecular structures | |||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: Each particle | |||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21401 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Details: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor, FSC / Details: METHOD--Local refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Details: Hydrogens have been added in their riding positions | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST
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