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- PDB-5lmp: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiatio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lmp | ||||||||||||||||||||||||||||||||
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Title | Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C) | ||||||||||||||||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
Specimen source | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
![]() | Hussain, T. / Llacer, J.L. / Wimberly, B.T. / Ramakrishnan, V. | ||||||||||||||||||||||||||||||||
![]() | Journal: Cell / Year: 2016 Title: Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. ![]() Abstract: In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 ...In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition. | ||||||||||||||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||
Date | Deposition: Aug 1, 2016 / Release: Oct 5, 2016
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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-Related structure data
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules AY
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source: (natural) ![]() ![]() ![]() |
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#24: RNA chain | ![]() Mass: 12525.466 Da / Num. of mol.: 1 / Source: (synth.) ![]() ![]() ![]() |
+30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
-Translation initiation factor IF- ... , 2 types, 2 molecules WX
#22: Protein/peptide | Mass: 8247.664 Da / Num. of mol.: 1 Source: (gene. exp.) ![]() ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infA, TTHA1669 / Production host: ![]() ![]() ![]() |
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#23: Protein/peptide | Mass: 19904.377 Da / Num. of mol.: 1 Source: (gene. exp.) ![]() ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infC, TTHA0551 / Production host: ![]() ![]() ![]() |
-Non-polymers , 2 types, 110 molecules 


#25: Chemical | ChemComp-MG / #26: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: ![]() |
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Sample preparation
Component | Name: 30S-IF1-IF3-mRNA pre-initiation complex (state-1C) / Type: RIBOSOME Entity ID: 1, Source: MULTIPLE SOURCES Molecular weight | Value: 0.8261 MDa / Experimental value: NO | Buffer solution | pH: 7.5 | Buffer component |
Specimen | Conc.: 0.08 / Embedding applied: NO / Shadowing applied: NO / Staining applied | ![]() ![]() Specimen support | Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil | Vitrification | ![]() Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 | |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Microscope model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Temperature (max): 100 / Temperature (min): 90 |
Image recording | Average exposure time: 1.1 / Electron dose: 30 Details: Recorded in a FEI Falcon III direct electron detector. Images were collected in movie-mode at 32 frames per second Film or detector model: OTHER / Number of grids imaged: 5 / Number of real images: 4400 |
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Processing
EM software |
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Image processing | Details: FEI Falcon III | ||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Number of particles selected: 666610 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.35 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18830 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: FSC |