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- PDB-6gsm: Structure of a partial yeast 48S preinitiation complex in open co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gsm | ||||||||||||
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Title | Structure of a partial yeast 48S preinitiation complex in open conformation. | ||||||||||||
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![]() | RIBOSOME / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / tRNAi / 48S PIC / small ribosome subunit | ||||||||||||
Function / homology | ![]() formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / eukaryotic translation initiation factor 2 complex ...formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / incipient cellular bud site / eukaryotic translation initiation factor 2 complex / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / 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) / 90S preribosome / regulation of translational fidelity / translation regulator activity / translational termination / 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 / translation initiation factor activity / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / 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 / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / 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 | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.15 Å | ||||||||||||
![]() | Llacer, J.L. / Hussain, T. / Gordiyenko, Y. / Ramakrishnan, V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Large-scale movement of eIF3 domains during translation initiation modulate start codon selection. Authors: Jose L Llácer / Tanweer Hussain / Jinsheng Dong / Laura Villamayor / Yuliya Gordiyenko / Alan G Hinnebusch / ![]() ![]() ![]() ![]() Abstract: The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single ...The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection. #1: ![]() 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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-Validation report
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-Related structure data
Related structure data | ![]() 0057MC ![]() 3049M ![]() 0058C ![]() 6gsnC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-RNA chain , 3 types, 3 molecules 123
#1: RNA chain | Mass: 24799.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 579239.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: RNA chain | Mass: 919.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVWYabcde
#3: Protein | Mass: 23140.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CN12 |
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#5: Protein | Mass: 26404.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CWD0 |
#8: Protein | Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CWJ2 |
#10: Protein | Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CM04 |
#11: Protein | Mass: 21033.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CTD6 |
#12: Protein | Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CMG3 |
#16: Protein | Mass: 12710.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CLU4 |
#18: Protein | Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: P27069 |
#20: Protein | Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q875N2 |
#25: Protein | Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CXT6 |
#26: Protein | Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CW21 |
#28: Protein | Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CU44 |
#30: Protein | Mass: 11166.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CS01 |
#31: Protein | Mass: 8753.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CNL2 |
#32: Protein | Mass: 6972.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: P33285 |
#33: Protein | Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CPG3 |
#34: Protein | Mass: 6608.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CUH5 |
-Protein , 16 types, 16 molecules CDFJKLNPRSTUXZfg
#6: Protein | Mass: 23162.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CKL3 |
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#7: Protein | Mass: 24830.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CRK7 |
#9: Protein | Mass: 22912.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CRA3 |
#13: Protein | Mass: 20882.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CM18 |
#14: Protein | Mass: 11423.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CVZ5 |
#15: Protein | Mass: 17712.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CX80 |
#17: Protein | Mass: 16858.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CJK0 |
#19: Protein | Mass: 13448.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CKV4 |
#21: Protein | Mass: 14200.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CWU3 |
#22: Protein | Mass: 16953.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CWT9 |
#23: Protein | Mass: 15747.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CXM0 |
#24: Protein | Mass: 12032.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CIM1 |
#27: Protein | Mass: 15916.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: F2Z602, UniProt: Q875M3*PLUS |
#29: Protein | Mass: 7939.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CW78 |
#35: Protein | Mass: 7958.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: P69061 |
#36: Protein | Mass: 35612.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q6CNI7 |
-Protein/peptide , 1 types, 1 molecules h
#37: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Eukaryotic translation initiation factor ... , 10 types, 10 molecules ijklmopqsr
#38: Protein | Mass: 10953.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#39: Protein | Mass: 30221.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#40: Protein | Mass: 47230.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#41: Protein | Mass: 16458.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#42: Protein | Mass: 10919.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#43: Protein | Mass: 62822.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#44: Protein | Mass: 75014.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#45: Protein | Mass: 76963.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#46: Protein | Mass: 38229.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#47: Protein/peptide | Mass: 5576.158 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 88 molecules ![](data/chem/img/7NO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GCP.gif)
#48: Chemical | ChemComp-7NO / [( | ||||
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#49: Chemical | ChemComp-MG / #50: Chemical | ChemComp-ZN / #51: Chemical | ChemComp-GCP / | |
-Details
Has ligand of interest | N |
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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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Molecular weight | Value: 1.8 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / 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 / Temperature (max): 100 K / Temperature (min): 90 K |
Image recording | Average exposure time: 1.1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2610 Details: Images were collected in movie-mode at 40 frames per second |
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Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: FEI Falcon III | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 360729 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5750 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSC | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 5.15→5.15 Å / Cor.coef. Fo:Fc: 0.535 / SU B: 368.377 / SU ML: 3.484 / ESU R: 1.194 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: 264.057 Å2
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Refinement step | Cycle: 1 / Total: 99882 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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