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 present a cryoelectron microscopy (cryo-EM) reconstruction at 3 ...

    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.



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50S RIBOSOMAL PROTEIN L32A [auth 0]56Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L33B [auth 1]50Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L34C [auth 2]46Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L35D [auth 3]64Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L36E [auth 4]38Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L10F [auth 5]148Escherichia coliMutation(s): 0 
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RIBOSOMAL L7 PROTEING [auth 6]30Escherichia coliMutation(s): 0 
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TRYPTOPHANASEH [auth 7]20Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L25I [auth 8]94Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L2L [auth C]271Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L11R [auth I]141Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L13S [auth J]142Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L14T [auth K]122Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L15U [auth L]143Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L16V [auth M]136Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L17W [auth N]120Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L18X [auth O]116Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L19Y [auth P]114Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L20Z [auth Q]117Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L21AA [auth R]103Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L23CA [auth T]93Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L24DA [auth U]102Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L27FA [auth W]79Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L28GA [auth X]77Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L29HA [auth Y]63Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L30IA [auth Z]58Escherichia coliMutation(s): 0 
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RRNA-23S RIBOSOMAL RNAJ [auth A]2,854Escherichia coli
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RRNA-5S RIBOSOMAL RNAK [auth B]118Escherichia coli
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RNAEA [auth V]77Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

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LA [auth 7],
MA [auth 7]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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KA [auth 4]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth 4],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth B],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth B],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth B],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth B],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth C],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth C],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth E],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
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  (Full details and data files)

  • 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