4UY8

Molecular basis for the ribosome functioning as a L-tryptophan sensor - Cryo-EM structure of a TnaC stalled E.coli ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Basis for the Ribosome Functioning as an L-Tryptophan Sensor.

Bischoff, L.Berninghausen, O.Beckmann, R.

(2014) Cell Rep 9: 469

  • DOI: 10.1016/j.celrep.2014.09.011
  • Primary Citation of Related Structures:  
    4UY8

  • PubMed Abstract: 
  • Elevated levels of the free amino acid L-tryptophan (L-Trp) trigger expression of the tryptophanase tnaCAB operon in E. coli. Activation depends on tryptophan-dependent ribosomal stalling during translation of the upstream TnaC peptide. Here, we pres ...

    Elevated levels of the free amino acid L-tryptophan (L-Trp) trigger expression of the tryptophanase tnaCAB operon in E. coli. Activation depends on tryptophan-dependent ribosomal stalling during translation of the upstream TnaC peptide. Here, we present a cryoelectron microscopy (cryo-EM) reconstruction at 3.8 Å resolution of a ribosome stalled by the TnaC peptide. Unexpectedly, we observe two L-Trp molecules in the ribosomal exit tunnel coordinated within composite hydrophobic pockets formed by the nascent TnaC peptide and the tunnel wall. As a result, the peptidyl transferase center (PTC) adopts a distinct conformation that precludes productive accommodation of release factor 2 (RF2), thereby inducing translational stalling. Collectively, our results demonstrate how the translating ribosome can act as a small molecule sensor for gene regulation.


    Organizational Affiliation

    Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany. Electronic address: beckmann@lmb.uni-muenchen.de.



Macromolecules

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Entity ID: 1
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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 L105148Escherichia coliMutation(s): 0 
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RIBOSOMAL L7 PROTEIN630Escherichia coliMutation(s): 0 
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TRYPTOPHANASE720Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L25894Escherichia 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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RIBOSOMAL PROTEIN L9H50Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L11I141Escherichia 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 L27W79Escherichia 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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RRNA-23S RIBOSOMAL RNAA2854Escherichia coli
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RRNA-5S RIBOSOMAL RNAB118Escherichia coli
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MoleculeChainsLengthOrganismImage
RNAV77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download CCD File 
7
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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

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4, A, B, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.3: 2018-10-03
    Changes: Data collection, Derived calculations