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- PDB-6fyx: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -
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Basic information
Entry | Database: PDB / ID: 6fyx | ||||||||||||
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Title | Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1) | ||||||||||||
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![]() | RIBOSOME / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / eIF5 / tRNAi / 48S PIC / small ribosome subunit | ||||||||||||
Function / homology | ![]() formation of translation initiation ternary complex / eukaryotic initiation factor eIF2 binding / 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 ...formation of translation initiation ternary complex / eukaryotic initiation factor eIF2 binding / 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 / GDP-dissociation inhibitor activity / regulation of translational initiation / 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 / 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) / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / rescue of stalled ribosome / GTPase activator activity / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / 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: 3.5 Å | ||||||||||||
![]() | Llacer, J.L. / Hussain, T. / Gordiyenko, Y. / Ramakrishnan, V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. Authors: Jose Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan / ![]() ![]() ![]() ![]() Abstract: In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) ...In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNA. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNA interaction influenced initiation at near-cognate UUG codons and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4327MC ![]() 4328C ![]() 4329C ![]() 4330C ![]() 4331C ![]() 6fyyC C: citing same article ( M: map data used to model this data |
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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: 24713.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 579454.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: rRNA modifications taken from: http://people.biochem.umass.edu/fournierlab/3dmodmap/ysssu2dframes43d.php Source: (natural) ![]() References: GenBank: 49642208 |
#3: RNA chain | Mass: 15344.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVWYabcde
#4: Protein | Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CN12 |
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#5: Protein | Mass: 29013.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CWD0 |
#8: Protein | Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CWJ2 |
#10: Protein | Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CM04 |
#11: Protein | Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CTD6 |
#12: Protein | Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CMG3 |
#16: Protein | Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CLU4 |
#18: Protein | Mass: 14530.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P27069 |
#20: Protein | Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q875N2 |
#25: Protein | Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CXT6 |
#26: Protein | Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CW21 |
#28: Protein | Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CU44 |
#30: Protein | Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CS01 |
#31: Protein | Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CNL2 |
#32: Protein | Mass: 7549.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P33285 |
#33: Protein | Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CPG3 |
#34: Protein | Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CUH5 |
-Protein , 17 types, 17 molecules CDFJKLNPRSTUXZfgq
#6: Protein | Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CKL3 |
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#7: Protein | Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CRK7 |
#9: Protein | Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CRA3 |
#13: Protein | Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CM18 |
#14: Protein | Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CVZ5 |
#15: Protein | Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CX80 |
#17: Protein | Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CJK0 |
#19: Protein | Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CKV4 |
#21: Protein | Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CWU3 |
#22: Protein | Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CWT9 |
#23: Protein | Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CXM0 |
#24: Protein | Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CIM1 |
#27: Protein | Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: F2Z602 |
#29: Protein | Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CW78 |
#35: Protein | Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P69061 |
#36: Protein | Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q6CNI7 |
#45: Protein | Mass: 86539.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
-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) ![]() References: UniProt: P0CX86 |
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-Eukaryotic translation initiation factor ... , 9 types, 9 molecules ijklmoprs
#38: Protein | Mass: 17462.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TIF11, YMR260C, YM8156.02C / Production host: ![]() ![]() |
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#39: Protein | Mass: 34763.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SUI2, TIF211, YJR007W, J1429 / Production host: ![]() ![]() |
#40: Protein | Mass: 57942.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GCD11, TIF213, YER025W / Production host: ![]() ![]() |
#41: Protein | Mass: 31631.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SUI3, TIF212, YPL237W / Production host: ![]() ![]() |
#42: Protein | Mass: 45321.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TIF5, YPR041W, YP3085.05 / Production host: ![]() ![]() |
#43: Protein | Mass: 110517.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: ![]() ![]() |
#44: Protein | Mass: 88241.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PRT1, CDC63, YOR361C / Production host: ![]() ![]() |
#46: Protein | Mass: 30520.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TIF35, SCY_1313 / Production host: ![]() ![]() |
#47: Protein | Mass: 38803.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TIF34, YMR146C, YM9375.16C / Production host: ![]() ![]() |
-Non-polymers , 4 types, 124 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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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 material: COPPER / Grid mesh size: 400 divisions/in. / 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: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / 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: 3 / Num. of real images: 3600 Details: Images were collected in movie-mode at 32 frames per second |
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Processing
Software | Name: REFMAC / Version: 5.8.0166 / 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: 706713 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74772 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 66 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSC | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.5→3.5 Å / Cor.coef. Fo:Fc: 0.901 / SU B: 11.473 / SU ML: 0.19 / ESU R: 0.274 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 162.552 Å2
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Refinement step | Cycle: 1 / Total: 104332 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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