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- EMDB-2773: Molecular basis for the ribosome functioning as a L-tryptophan se... -

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Basic information

Entry
Database: EMDB / ID: EMD-2773
TitleMolecular basis for the ribosome functioning as a L-tryptophan sensor - Cryo-EM structure of a TnaC stalled E.coli ribosome
Map dataCryo-EM structure of a TnaC stalled ribosome
Sample
  • Sample: TnaC stalled E.coli ribosome
  • Complex: E.coli ribosome
  • Protein or peptide: Tryptophanase leader peptide
KeywordsTnaC / stalled ribosome / Cryo-EM / translation regulation
Function / homology
Function and homology information


positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / t-UTP complex / rDNA heterochromatin / tryptophan catabolic process / rRNA methylation / positive regulation of transcription by RNA polymerase I / stringent response / Major pathway of rRNA processing in the nucleolus and cytosol / transcriptional attenuation ...positive regulation of tryptophan metabolic process / transcriptional attenuation by ribosome / t-UTP complex / rDNA heterochromatin / tryptophan catabolic process / rRNA methylation / positive regulation of transcription by RNA polymerase I / stringent response / Major pathway of rRNA processing in the nucleolus and cytosol / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / small-subunit processome / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / : / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain ...Tryptophanese operon leader peptide / Tryptophanase operon leader peptide / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 5 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L3 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / : / 50S ribosomal protein L10 / 50S ribosomal protein L22 / : ...U3 small nucleolar RNA-associated protein 5 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L3 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / : / 50S ribosomal protein L10 / 50S ribosomal protein L22 / : / 50S ribosomal protein L25 / : / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Tryptophanase operon leader peptide / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25 / : / : / L8 / : / : / : / : / : / : / : / : / : / : / : / : / : / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBischoff L / Berninghausen O / Beckmann R
CitationJournal: Cell Rep / Year: 2014
Title: Molecular basis for the ribosome functioning as an L-tryptophan sensor.
Authors: Lukas Bischoff / Otto Berninghausen / Roland Beckmann /
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 ...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.
History
DepositionAug 29, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseOct 22, 2014-
UpdateNov 19, 2014-
Current statusNov 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4uy8
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2773.jpg

Downloads & links

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Map

FileDownload / File: emd_2773.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a TnaC stalled ribosome
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy EMDB: 0.9 / Movie #1: 0.6
Minimum - Maximum-2.71148705 - 3.35368133
Average (Standard dev.)-0.00110617 (±0.18318665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 404.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z404.800404.800404.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-2.7113.354-0.001

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Supplemental data

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Sample components

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Entire : TnaC stalled E.coli ribosome

EntireName: TnaC stalled E.coli ribosome
Components
  • Sample: TnaC stalled E.coli ribosome
  • Complex: E.coli ribosome
  • Protein or peptide: Tryptophanase leader peptide

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Supramolecule #1000: TnaC stalled E.coli ribosome

SupramoleculeName: TnaC stalled E.coli ribosome / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: E.coli ribosome

SupramoleculeName: E.coli ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KC6

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Macromolecule #1: Tryptophanase leader peptide

MacromoleculeName: Tryptophanase leader peptide / type: protein_or_peptide / ID: 1 / Name.synonym: TnaC / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJan 27, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3000 / Bits/pixel: 32
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 72468

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