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- EMDB-58124: In situ subtomogram average of a ribosome bound to ribosome assoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-58124
TitleIn situ subtomogram average of a ribosome bound to ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen (mNeon-KDEL)
Map dataIn situ subtomogram average of a ribosome bound to a ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen (mNeon-KDEL).
Sample
  • Complex: Ribosome bound to ribosome associated vesicle
KeywordsIn situ / RAV / Neuron / cryo-ET / STA / RIBOSOME
Biological speciesRattus (rats)
Methodsubtomogram averaging / cryo EM / Resolution: 22.0 Å
AuthorsCarter SD / Jensen GJ / Freyberg Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R35GM122588 United States
CitationJournal: bioRxiv / Year: 2024
Title: Ribosome-Associated Vesicles promote activity-dependent local translation.
Authors: Eva Martin-Solana / Stephen D Carter / Eric K F Donahue / Jiying Ning / Jill R Glausier / Matias A Preisegger / Leanna Eisenman / Paul N Joseph / Cedric Bouchet-Marquis / Ken Wu / Catherina ...Authors: Eva Martin-Solana / Stephen D Carter / Eric K F Donahue / Jiying Ning / Jill R Glausier / Matias A Preisegger / Leanna Eisenman / Paul N Joseph / Cedric Bouchet-Marquis / Ken Wu / Catherina L Mobini / Amber N Frantz / Stephanie Puig / Cheri M Hampton / Nadine Kabbani / Grant J Jensen / Simon C Watkins / Karl Deisseroth / Lief E Fenno / Michael S Gold / Zachary P Wills / Kristopher Burkewitz / Sulagna Das / Zachary Freyberg /
Abstract: Local protein synthesis in axons and dendrites underpins synaptic plasticity. However, the composition of the protein synthesis machinery in distal neuronal processes and the mechanisms for its ...Local protein synthesis in axons and dendrites underpins synaptic plasticity. However, the composition of the protein synthesis machinery in distal neuronal processes and the mechanisms for its activity-driven deployment to local translation sites remain unclear. Here, we employed cryo-electron tomography, volume electron microscopy, and live-cell imaging to identify Ribosome-Associated Vesicles (RAVs) as a dynamic platform for moving ribosomes to distal processes. Stimulation via chemically-induced long-term potentiation causes RAV accumulation in distal sites to drive local translation. We also demonstrate activity-driven changes in RAV generation and dynamics , identifying tubular ER shaping proteins in RAV biogenesis. Together, our work identifies a mechanism for ribosomal delivery to distal sites in neurons to promote activity-dependent local translation.
History
DepositionMay 15, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58124.png

Downloads & links

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Map

FileDownload / File: emd_58124.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ subtomogram average of a ribosome bound to a ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen (mNeon-KDEL).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.65 Å/pix.
x 168 pix.
= 445.2 Å		2.65 Å/pix.
x 168 pix.
= 445.2 Å		2.65 Å/pix.
x 168 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.703
Minimum - Maximum-6.4135127 - 5.4192586
Average (Standard dev.)0.024455456 (±0.5397118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin353535
Dimensions168168168
Spacing168168168
CellA=B=C: 445.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 (unmasked) of an in situ...

Fileemd_58124_half_map_1.map
AnnotationHalf map 1 (unmasked) of an in situ subtomogram average of a ribosome bound to a ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen (mNeon-KDEL).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 (unmasked) of an in situ...

Fileemd_58124_half_map_2.map
AnnotationHalf map 2 (unmasked) of an in situ subtomogram average of a ribosome bound to a ribosome associated vesicle in primary neurons expressing KDEL tagged with mNeonGreen (mNeon-KDEL).
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 bound to ribosome associated vesicle

EntireName: Ribosome bound to ribosome associated vesicle
Components
  • Complex: Ribosome bound to ribosome associated vesicle

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Supramolecule #1: Ribosome bound to ribosome associated vesicle

SupramoleculeName: Ribosome bound to ribosome associated vesicle / type: complex / ID: 1 / Parent: 0
Details: Freshly isolated neurons were plated onto sterile, poly-D-lysine/laminin-coated 200 mesh Quantifoil R2/2 gold NH2 London finder grids (200 mesh)
Source (natural)Organism: Rattus (rats) / Organ: Brain / Tissue: Hippocampal neurons

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
Details: Neurons were maintained in neurobasal medium supplemented with B27 (2%), penicillin/streptomycin (100 mg/mL), and 2 mM glutamine with two-fifths of the media replaced every 4 days (37C, 5% CO2).
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 5
VitrificationCryogen name: ETHANE-PROPANE
DetailsFreshly isolated hippocampal neurons were plated onto sterile, poly-D-lysine/laminin-coated 200 mesh Quantifoil R2/2 gold NH2 London finder grids (200 mesh), and transfected with KDEL tagged with mNeonGreen (mNeon-KDEL)

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 164
ExtractionNumber tomograms: 5 / Number images used: 164 / Method: EMAN2 / Software - Name: EMAN2
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: EMAN2
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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