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- EMDB-13975: Neuronal RNA granules are ribosome complexes stalled at the pre-t... -

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Basic information

Entry
Database: EMDB / ID: EMD-13975
TitleNeuronal RNA granules are ribosome complexes stalled at the pre-translocation state
Map dataRibosome structure from the intact RNA granules
Sample
  • Complex: Ribosome structure in the rat cortex-hippocampus derived intact neuronal RNA granules.
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsPulk A
Funding support Estonia, 3 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)IG 3911 Estonia
Estonian Research CouncilPSG87 Estonia
Estonian Research CouncilMOBTP44 Estonia
CitationJournal: J Mol Biol / Year: 2022
Title: Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state.
Authors: Kalle Kipper / Abbas Mansour / Arto Pulk /
Abstract: The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA- ...The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome-containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified a potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion.
History
DepositionDec 13, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13975.png

Downloads & links

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Map

FileDownload / File: emd_13975.map.gz / Format: CCP4 / Size: 48.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRibosome structure from the intact RNA granules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 234 pix.
= 379.08 Å		1.62 Å/pix.
x 234 pix.
= 379.08 Å		1.62 Å/pix.
x 234 pix.
= 379.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0588
Minimum - Maximum-0.2605123 - 0.45730248
Average (Standard dev.)0.0058582793 (±0.031516615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions234234234
Spacing234234234
CellA=B=C: 379.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13975_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ribosome structure in the rat cortex-hippocampus derived intact n...

EntireName: Ribosome structure in the rat cortex-hippocampus derived intact neuronal RNA granules.
Components
  • Complex: Ribosome structure in the rat cortex-hippocampus derived intact neuronal RNA granules.

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Supramolecule #1: Ribosome structure in the rat cortex-hippocampus derived intact n...

SupramoleculeName: Ribosome structure in the rat cortex-hippocampus derived intact neuronal RNA granules.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#83
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Brain / Tissue: Cortex and hippocampus / Organelle: RNA granule

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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: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKOAcpotassium acetate
4.0 mMMgOAcmagnesium acetate
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 30.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1144 / Average exposure time: 1.2 sec. / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 176232
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

0600

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 97082
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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