5LZB

Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the initial binding state (IB)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



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 ne ...

    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.



Macromolecules

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Entity ID: 2
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30S ribosomal protein S2b218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3c206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4d205Escherichia coliMutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S5e157Escherichia coliMutation(s): 0 
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30S ribosomal protein S6f100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7g151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8h129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9i127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10j98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11k116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12l123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13m114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14n100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15o88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16p82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17q80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18r65Escherichia coliMutation(s): 0 
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30S ribosomal protein S19s79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20t85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21u65Escherichia coliMutation(s): 0 
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Selenocysteine-specific elongation factorz614Escherichia coliMutation(s): 0 
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50S ribosomal protein L2C271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3D209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4E201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5F177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6G176Escherichia coliMutation(s): 0 
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50S ribosomal protein L11I141Escherichia coliMutation(s): 0 
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50S ribosomal protein L9H149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13J142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15L143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17N120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18O116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19P114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20Q117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21R103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22S110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23T93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W75Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29Y63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Z58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32056Escherichia coliMutation(s): 0 
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50S ribosomal protein L33150Escherichia coliMutation(s): 0 
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50S ribosomal protein L34246Escherichia coliMutation(s): 0 
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50S ribosomal protein L35364Escherichia coliMutation(s): 0 
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50S ribosomal protein L36438Escherichia coliMutation(s): 0 
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50S ribosomal protein L31666Escherichia coliMutation(s): 0 
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16S ribosomal RNAa1539Escherichia coli
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Entity ID: 22
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fMet-tRNAfMetv77Escherichia coli
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SECIS mRNAx48Escherichia coli
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Sec-tRNASecy95Escherichia coli
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23S ribosomal RNAA2903Escherichia coli
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5S ribosomal RNAB120Escherichia coli
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  • Entity ID: 58
    MoleculeChainsLengthOrganismImage
    CCA 3' end of E-site tRNASec (low occupancy)w3Escherichia coli
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

    Download CCD File 
    z
    PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    FME
    Query on FME

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    v
    N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    SEC
    Query on SEC

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    y
    SELENOCYSTEINE
    C3 H7 N O2 Se
    ZKZBPNGNEQAJSX-REOHCLBHSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    4, 6
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    z
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 5.30 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 

    • 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, Structure summary