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- EMDB-54447: Subtomogram average of synaptic microtubule from rat hippocampal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54447
TitleSubtomogram average of synaptic microtubule from rat hippocampal neurons
Map dataSubtomogram average of synaptic microtubule from rat hippocampal neurons
Sample
  • Complex: Subtomogram average of synaptic microtubule from FIB-milled hippocampal neurons
Keywordssynapse / microtubule / cytoskeleton / CYTOSOLIC PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsPetrovic A / Do TT / Siegert A / Fernandez-Busnadiego R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)1286 Germany
CitationJournal: Structure / Year: 2026
Title: A correlative workflow for synaptic imaging by cryo-electron tomography.
Authors: Thanh Thao Do / Anna Siegert / Florelle Domart / Fabienne Hahn / Christina Zeising / Sarah Muth / Constantin Pape / Kathrin Kusch / Thomas Dresbach / Silvio O Rizzoli / Arsen Petrovic / ...Authors: Thanh Thao Do / Anna Siegert / Florelle Domart / Fabienne Hahn / Christina Zeising / Sarah Muth / Constantin Pape / Kathrin Kusch / Thomas Dresbach / Silvio O Rizzoli / Arsen Petrovic / Rubén Fernández-Busnadiego /
Abstract: Despite decades of intense research, the molecular organization of the synapse is not well understood. To address this issue, we sought to develop a method for systematic imaging of synapses by cryo- ...Despite decades of intense research, the molecular organization of the synapse is not well understood. To address this issue, we sought to develop a method for systematic imaging of synapses by cryo-electron tomography (cryo-ET), a technology capable of mapping cellular architecture at molecular resolution. Thinning of cellular samples by cryo-focused ion beam milling is a prerequisite for high-quality cryo-ET imaging, but this process needs to be guided to the structures of interest. To allow synaptic targeting, we established a correlative cryo-light/electron microscopy approach by which synapses are fluorescently labeled in a minimally invasive manner, using a synthetic binder of the postsynaptic scaffold PSD-95 and antibodies against the presynaptic protein synaptotagmin-1. Cryo-ET imaging at sites of colocalization predominantly revealed excitatory synapses. Our method allows structural studies of synapse-resident protein complexes in situ, facilitating investigations of the molecular architecture of synapses.
History
DepositionJul 18, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54447.png

Downloads & links

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Map

FileDownload / File: emd_54447.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of synaptic microtubule from rat hippocampal neurons
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.78 Å/pix.
x 128 pix.
= 483.84 Å		3.78 Å/pix.
x 128 pix.
= 483.84 Å		3.78 Å/pix.
x 128 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0854
Minimum - Maximum-0.14865898 - 0.23378395
Average (Standard dev.)0.0027776223 (±0.038227327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 483.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54447_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: half map

Fileemd_54447_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_54447_half_map_2.map
Annotationhalf 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 : Subtomogram average of synaptic microtubule from FIB-milled hippo...

EntireName: Subtomogram average of synaptic microtubule from FIB-milled hippocampal neurons
Components
  • Complex: Subtomogram average of synaptic microtubule from FIB-milled hippocampal neurons

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Supramolecule #1: Subtomogram average of synaptic microtubule from FIB-milled hippo...

SupramoleculeName: Subtomogram average of synaptic microtubule from FIB-milled hippocampal neurons
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 statefilament

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 3.0 µm / Calibrated magnification: 64000 / Illumination 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: 64000
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number subtomograms used: 50000
ExtractionNumber tomograms: 18 / Number images used: 100000 / Reference model: de novo / Software - Name: STOPGAP
CTF correctionSoftware - Name: IMOD (ver. 11.4) / Type: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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