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- EMDB-4799: B.subtilis 50S subunit-nascent chain-tRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4799
TitleB.subtilis 50S subunit-nascent chain-tRNA complex
Map data
SampleBacillus subtilis 50S subunit-nascent chain-tRNA complex
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLytvynenko I / Paternoga H / Thrun A / Balke A / Mueller T / Nagler K / Chiang CH / Tsaprailis G / Anders S / Maupin-Furlow JA / Bischofs I / Spahn CMT / Joazeiro CAP
CitationJournal: Cell / Year: 2019
Title: Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control.
Authors: Iryna Lytvynenko / Helge Paternoga / Anna Thrun / Annika Balke / Tina A Müller / Christina H Chiang / Katja Nagler / George Tsaprailis / Simon Anders / Ilka Bischofs / Julie A Maupin-Furlow / Christian M T Spahn / Claudio A P Joazeiro /
Abstract: In ribosome-associated quality control (RQC), Rqc2/NEMF closely supports the E3 ligase Ltn1/listerin in promoting ubiquitylation and degradation of aberrant nascent-chains obstructing large (60S) ...In ribosome-associated quality control (RQC), Rqc2/NEMF closely supports the E3 ligase Ltn1/listerin in promoting ubiquitylation and degradation of aberrant nascent-chains obstructing large (60S) ribosomal subunits-products of ribosome stalling during translation. However, while Ltn1 is eukaryote-specific, Rqc2 homologs are also found in bacteria and archaea; whether prokaryotic Rqc2 has an RQC-related function has remained unknown. Here, we show that, as in eukaryotes, a bacterial Rqc2 homolog (RqcH) recognizes obstructed 50S subunits and promotes nascent-chain proteolysis. Unexpectedly, RqcH marks nascent-chains for degradation in a direct manner, by appending C-terminal poly-alanine tails that act as degrons recognized by the ClpXP protease. Furthermore, RqcH acts redundantly with tmRNA/ssrA and protects cells against translational and environmental stresses. Our results uncover a proteolytic-tagging mechanism with implications toward the function of related modifications in eukaryotes and suggest that RQC was already active in the last universal common ancestor (LUCA) to help cope with incomplete translation.
DateDeposition: Apr 10, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4799.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 300 pix.
= 375. Å
1.25 Å/pix.
x 300 pix.
= 375. Å
1.25 Å/pix.
x 300 pix.
= 375. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density
Contour LevelBy AUTHOR: 2.1 / Movie #1: 2.1
Minimum - Maximum-3.370362 - 15.4463005
Average (Standard dev.)0.29348975 (±0.68866533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 375.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z375.000375.000375.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-3.37015.4460.293

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Supplemental data

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Sample components

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Entire Bacillus subtilis 50S subunit-nascent chain-tRNA complex

EntireName: Bacillus subtilis 50S subunit-nascent chain-tRNA complex
Number of components: 1

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Component #1: protein, Bacillus subtilis 50S subunit-nascent chain-tRNA complex

ProteinName: Bacillus subtilis 50S subunit-nascent chain-tRNA complex
Recombinant expression: No
MassTheoretical: 25 kDa
SourceSpecies: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (engineered)Expression System: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 44212
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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