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- EMDB-18341: ApdA-SRC with P-tRNA only -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18341
TitleApdA-SRC with P-tRNA only
Map dataPostprocessed final map
Sample
  • Complex: B. subtilis ApdA-stalled ribosomal complex
KeywordsStalling / Nascent chain / elongation arrest / regulation / RIBOSOME
Biological speciesAmycolatopsis japonica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsMorici M / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.
Authors: Martino Morici / Sara Gabrielli / Keigo Fujiwara / Helge Paternoga / Bertrand Beckert / Lars V Bock / Shinobu Chiba / Daniel N Wilson /
Abstract: Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein ...Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.
History
DepositionAug 30, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18341.png

Downloads & links

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Map

FileDownload / File: emd_18341.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed final map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å		0.82 Å/pix.
x 420 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.14416163 - 0.33346608
Average (Standard dev.)0.0010753971 (±0.009729683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Preprocessed map

Fileemd_18341_additional_1.map
AnnotationPreprocessed map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_18341_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18341_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : B. subtilis ApdA-stalled ribosomal complex

EntireName: B. subtilis ApdA-stalled ribosomal complex
Components
  • Complex: B. subtilis ApdA-stalled ribosomal complex

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Supramolecule #1: B. subtilis ApdA-stalled ribosomal complex

SupramoleculeName: B. subtilis ApdA-stalled ribosomal complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#49
Source (natural)Organism: Amycolatopsis japonica (bacteria)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: An unpublished map from our group was initially low-pass filtered and used as model, since the biology was analogous
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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