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- EMDB-12986: Control sample rancRNA_18 -

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Basic information

Entry
Database: EMDB / ID: EMD-12986
TitleControl sample rancRNA_18
Map datapostrpocessed 60S all particles
Sample
  • Complex: control sample for rancRNA_18 - cryoEM analysis and classification
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsZuber B / Iacovache I
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166527 Switzerland
Swiss National Science Foundation310030_188969 Switzerland
Swiss National Science Foundation163761 Switzerland
CitationJournal: RNA Biol / Year: 2021
Title: A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics.
Authors: Julia Reuther / Lukas Schneider / Ioan Iacovache / Andreas Pircher / Walid H Gharib / Benoît Zuber / Norbert Polacek /
Abstract: Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited ...Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited for allowing a swift response to changing environments and are therefore considered pivotal during the first wave of stress adaptation. Previously, we identified an mRNA-derived 18 nucleotides long rancRNA (rancRNA_18) in that rapidly downregulates protein synthesis during hyperosmotic stress. However, the molecular mechanism of action remained enigmatic. Here, we combine biochemical, genetic, transcriptome-wide and structural evidence, thus revealing rancRNA_18 as global translation inhibitor by targeting the E-site region of the large ribosomal subunit. Ribosomes carrying rancRNA_18 possess decreased affinity for A-site tRNA and impaired structural dynamics. Cumulatively, these discoveries reveal the mode of action of a rancRNA involved in modulating protein biosynthesis at a thus far unequalled precision.
History
DepositionMay 21, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12986.png

Downloads & links

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Map

FileDownload / File: emd_12986.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostrpocessed 60S all particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 450 pix.
= 473.4 Å		1.05 Å/pix.
x 450 pix.
= 473.4 Å		1.05 Å/pix.
x 450 pix.
= 473.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05366557 - 0.15802403
Average (Standard dev.)0.0010119376 (±0.006217919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 473.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z473.400473.400473.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0540.1580.001

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Supplemental data

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Additional map: 2D classification C5

Fileemd_12986_additional_1.map
Annotation2D classification C5
Projections & Slices
AxesZYX

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Additional map: 2D classification C6

Fileemd_12986_additional_2.map
Annotation2D classification C6
Projections & Slices
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Additional map: Refinement 80s all particles

Fileemd_12986_additional_3.map
AnnotationRefinement 80s all particles
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: 2D classification C10

Fileemd_12986_additional_4.map
Annotation2D classification C10
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 2D classification C8

Fileemd_12986_additional_5.map
Annotation2D classification C8
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 : control sample for rancRNA_18 - cryoEM analysis and classification

EntireName: control sample for rancRNA_18 - cryoEM analysis and classification
Components
  • Complex: control sample for rancRNA_18 - cryoEM analysis and classification

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Supramolecule #1: control sample for rancRNA_18 - cryoEM analysis and classification

SupramoleculeName: control sample for rancRNA_18 - cryoEM analysis and classification
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: trm10d

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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

Concentration0.1 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMTrisTris
100.0 mMKOAcKOAc
2.0 mMMg(OAc)2Mg(OAc)2
5.0 mMKOAcKOAc
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.25 mm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j7r

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 328615
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 10
FSC plot (resolution estimation)

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