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- EMDB-48113: Type B receptor-like particle on the postsynaptic membrane of syn... -

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Basic information

Entry
Database: EMDB / ID: EMD-48113
TitleType B receptor-like particle on the postsynaptic membrane of synaptosomes
Map data
Sample
  • Complex: Type B receptor-like particle on the postsynaptic membrane of synaptosomes
KeywordsSynaptosome / Postsynaptic / Receptor-like / Excitatory synapse / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsRong S / Qiangjun Z
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH132918 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R00MH113764 United States
CitationJournal: J Cell Biol / Year: 2025
Title: The postsynaptic density in excitatory synapses is composed of clustered, heterogeneous nanoblocks.
Authors: Rong Sun / James P Allen / Zhuqing Mao / Liana Wilson / Mariam Haider / Baris Alten / Zimeng Zhou / Xinyi Wang / Qiangjun Zhou /
Abstract: The nanoscale organization of proteins within synapses is critical for maintaining and regulating synaptic transmission and plasticity. Here, we used cryo-electron tomography (cryo-ET) to directly ...The nanoscale organization of proteins within synapses is critical for maintaining and regulating synaptic transmission and plasticity. Here, we used cryo-electron tomography (cryo-ET) to directly visualize the three-dimensional architecture and supramolecular organization of postsynaptic components in both synaptosomes and synapses from cultured neurons. Cryo-ET revealed that postsynaptic density (PSD) is composed of membrane-associated nanoblocks of various sizes. Subtomogram averaging from synaptosomes showed two types (type A and B) of postsynaptic receptor-like particles at resolutions of 24 and 26 Å, respectively. Furthermore, our analysis suggested that potential presynaptic release sites are closer to nanoblocks with type A/B receptor-like particles than to nanoblocks without type A/B receptor-like particles. The results of this study provide a more comprehensive understanding of synaptic ultrastructure and suggest that PSD is composed of clustering of various nanoblocks. These nanoblocks are heterogeneous in size, assembly, and distribution, which likely contribute to the dynamic nature of PSD in modulating synaptic strength.
History
DepositionDec 1, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48113.png

Downloads & links

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Map

FileDownload / File: emd_48113.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 96 pix.
= 316.8 Å		3.3 Å/pix.
x 96 pix.
= 316.8 Å		3.3 Å/pix.
x 96 pix.
= 316.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.26323354 - 0.80847853
Average (Standard dev.)0.1039059 (±0.19932589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48113_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_48113_half_map_2.map
Projections & Slices
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Sample components

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Entire : Type B receptor-like particle on the postsynaptic membrane of syn...

EntireName: Type B receptor-like particle on the postsynaptic membrane of synaptosomes
Components
  • Complex: Type B receptor-like particle on the postsynaptic membrane of synaptosomes

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Supramolecule #1: Type B receptor-like particle on the postsynaptic membrane of syn...

SupramoleculeName: Type B receptor-like particle on the postsynaptic membrane of synaptosomes
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 189
ExtractionNumber tomograms: 28 / Number images used: 1565
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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