5LZF

Structure of the 70S ribosome with fMetSec-tRNASec in the hybrid pre-translocation state (H)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The pathway to GTPase activation of elongation factor SelB on the ribosome.

Fischer, N.Neumann, P.Bock, L.V.Maracci, C.Wang, Z.Paleskava, A.Konevega, A.L.Schroder, G.F.Grubmuller, H.Ficner, R.Rodnina, M.V.Stark, H.

(2016) Nature 540: 80-85

  • DOI: 10.1038/nature20560
  • Primary Citation of Related Structures:  
    5LZB, 5LZA, 5LZD, 5LZC, 5LZF, 5LZE

  • PubMed Abstract: 
  • In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA Sec ) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA Sec recodes a UGA stop codon next to a downstream mRNA stem-loop ...

    In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA Sec ) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA Sec recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA Sec binding by SelB and show large-scale rearrangements of Sec-tRNA Sec . Upon initial binding of SelB-Sec-tRNA Sec to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA Sec covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA Sec away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.


    Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.



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Entity ID: 2
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30S ribosomal protein S2B [auth b]218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3C [auth c]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4D [auth d]205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5E [auth e]157Escherichia coliMutation(s): 0 
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30S ribosomal protein S6F [auth f]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7G [auth g]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8H [auth h]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9I [auth i]127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10J [auth j]98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11K [auth k]116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12L [auth l]123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13M [auth m]114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth n]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15O [auth o]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17Q [auth q]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18R [auth r]65Escherichia coliMutation(s): 0 
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30S ribosomal protein S19S [auth s]86Escherichia coliMutation(s): 0 
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30S ribosomal protein S20T [auth t]85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21U [auth u]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L2AA [auth C]271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BA [auth D]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4CA [auth E]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5DA [auth F]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6EA [auth G]176Escherichia coliMutation(s): 0 
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50S ribosomal protein L11FA [auth I]141Escherichia coliMutation(s): 0 
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50S ribosomal protein L9GA [auth H]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13HA [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14IA [auth K]122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15JA [auth L]143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16KA [auth M]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17LA [auth N]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18MA [auth O]116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19NA [auth P]114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20OA [auth Q]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21PA [auth R]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22QA [auth S]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23RA [auth T]93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24SA [auth U]102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25TA [auth V]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27UA [auth W]75Escherichia coliMutation(s): 0 
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50S ribosomal protein L28VA [auth X]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29WA [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L30XA [auth Z]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32YA [auth 0]56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33ZA [auth 1]50Escherichia coliMutation(s): 0 
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50S ribosomal protein L34AB [auth 2]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35BB [auth 3]64Escherichia coliMutation(s): 0 
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50S ribosomal protein L36CB [auth 4]38Escherichia coliMutation(s): 0 
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50S ribosomal protein L31DB [auth 6]66Escherichia coliMutation(s): 0 
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16S ribosomal RNAA [auth a]1539Escherichia coli
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Entity ID: 22
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tRNAfMetV [auth v]77Escherichia coli
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Entity ID: 23
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SECIS mRNAW [auth x]48Escherichia coli
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Entity ID: 24
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fMetSec-tRNASecX [auth y]95Escherichia coli
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Entity ID: 25
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23S ribosomal RNAY [auth A]2903Escherichia coli
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Entity ID: 26
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5S ribosomal RNAZ [auth B]120Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EB [auth 4], FB [auth 6]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanySonderforschungsbereich 860

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 2.0: 2019-02-20
    Changes: Data collection, Derived calculations, Polymer sequence