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- EMDB-82115: In Situ Subtomogram Average of the 80S Ribosome in Rat Hippocampa... -

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Basic information

Entry
Database: EMDB / ID: EMD-82115
TitleIn Situ Subtomogram Average of the 80S Ribosome in Rat Hippocampal Synapses
Map data
Sample
  • Cell: Primary cultured rat hippocampal neurons
    • Complex: 60S large ribosomal subunit
    • Complex: 40S small ribosomal subunit
Keywords80S Ribosome / Synaptic ribosomes / Protein synthesis / Hippocampal synapses / In situ / RIBOSOME
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsXia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP ...Xia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP / Rong CYL / Liu YT / Zhou ZH / Zhang XK / Wang PY / Lau PM / Bi GQ / Tao CL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Compartment-specific organization and activity-dependent remodeling of ribosomes in hippocampal synapses
Authors: Xia YN / Yan YT / Si Z / Wu J / Gu ML / Tian CL / Lu ZH / Liu S / Huang WL / Tang PP / Rong CYL / Liu YT / Zhou ZH / Zhang XK / Wang PY / Lau PM / Bi GQ / Tao CL
History
DepositionJul 15, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_82115.png

Downloads & links

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Map

FileDownload / File: emd_82115.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.57 Å/pix.
x 64 pix.
= 548.544 Å		8.57 Å/pix.
x 64 pix.
= 548.544 Å		8.57 Å/pix.
x 64 pix.
= 548.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.194
Minimum - Maximum-0.6293385 - 1.3812023
Average (Standard dev.)0.0051505575 (±0.1747573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 548.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_82115_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_82115_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_82115_half_map_2.map
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 : Primary cultured rat hippocampal neurons

EntireName: Primary cultured rat hippocampal neurons
Components
  • Cell: Primary cultured rat hippocampal neurons
    • Complex: 60S large ribosomal subunit
    • Complex: 40S small ribosomal subunit

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Supramolecule #1: Primary cultured rat hippocampal neurons

SupramoleculeName: Primary cultured rat hippocampal neurons / type: cell / ID: 1 / Parent: 0
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus

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Supramolecule #2: 60S large ribosomal subunit

SupramoleculeName: 60S large ribosomal subunit / type: complex / ID: 2 / Parent: 1
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus
Molecular weightTheoretical: 2.8 MDa

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Supramolecule #3: 40S small ribosomal subunit

SupramoleculeName: 40S small ribosomal subunit / type: complex / ID: 3 / Parent: 1
Details: Primary hippocampal neurons cultured in vitro from Sprague-Dawley (CD(SD) IGS) rats
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley (CD(SD) IGS) / Organ: brain / Tissue: hippocampus
Molecular weightTheoretical: 1.5 MDa

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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: 3.7
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
Details: The grids were plasma treated to render the carbon support film hydrophilic before sample application.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 307 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 3.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 14091
ExtractionNumber tomograms: 275 / Number images used: 20363 / Software - Name: RELION (ver. 3.1)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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