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- EMDB-55741: in situ subtomogram average of TRiC particles from dopaminergic v... -

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Basic information

Entry
Database: EMDB / ID: EMD-55741
Titlein situ subtomogram average of TRiC particles from dopaminergic varicosities
Map datain situ subtomogram average of TRiC particles from dopaminergic varicosities
Sample
  • Complex: TRiC particles from dopaminergic varicosities
KeywordsTRiC / TRiC-CCT / TRiC/CCT / CCT/TRiC / TRiC chaperone / The chaperonin-containing TCP-1 (CCT) complex. / CYTOSOLIC PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsLycas MD / Morado DR / Briggs JAG / Erlendsson S
Funding support Denmark, Germany, 5 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0030788 Denmark
LundbeckfondenR230-2016-3154 Denmark
LundbeckfondenR276-2018-792 Denmark
LundbeckfondenR359-2020-2301 Denmark
Max Planck Societynone Germany
CitationJournal: J Cell Biol / Year: 2026
Title: Ultrastructure of dopaminergic varicosities revealed by cryo-correlative light and electron microscopy.
Authors: Matthew Domenic Lycas / Dustin R Morado / Ulrik Gether / John A G Briggs / Simon Erlendsson /
Abstract: Dopaminergic neurons are fundamental in governing motivation, movement, and many aspects of cognition. The targeted modulation of dopaminergic signaling serves as a cornerstone in developing ...Dopaminergic neurons are fundamental in governing motivation, movement, and many aspects of cognition. The targeted modulation of dopaminergic signaling serves as a cornerstone in developing therapeutic interventions for conditions such as Parkinson's disease, schizophrenia, and addiction. Despite the pivotal role of dopaminergic neurons, the ultrastructure of dopaminergic synapses remains poorly understood. Here, we establish and utilize a cryo-correlative light and electron microscopy process to investigate the micro/nanoscale architecture and organelle content of dopaminergic varicosities. Using cryo-electron tomography and subtomogram averaging, we demonstrate the ability to resolve in situ complex structures of the TRiC/CCT chaperone and the vacuolar-type ATPase. We combine our experimental setup with pharmacological treatments using dopamine or haloperidol, showing bidirectional modulation of vesicular content and mitochondrial calcium phosphate deposition. These findings contribute to our understanding of the composition and (re)organization of dopaminergic varicosities and provide a methodological platform for further studies of the structure and cell biology of dopaminergic neurons and their responses.
History
DepositionNov 17, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55741.png

Downloads & links

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Map

FileDownload / File: emd_55741.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationin situ subtomogram average of TRiC particles from dopaminergic varicosities
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.38 Å/pix.
x 64 pix.
= 216.32 Å		3.38 Å/pix.
x 64 pix.
= 216.32 Å		3.38 Å/pix.
x 64 pix.
= 216.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.11135532 - 0.6056005
Average (Standard dev.)0.07177641 (±0.15676397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half1

Fileemd_55741_half_map_1.map
AnnotationHalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2

Fileemd_55741_half_map_2.map
AnnotationHalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRiC particles from dopaminergic varicosities

EntireName: TRiC particles from dopaminergic varicosities
Components
  • Complex: TRiC particles from dopaminergic varicosities

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Supramolecule #1: TRiC particles from dopaminergic varicosities

SupramoleculeName: TRiC particles from dopaminergic varicosities / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Backside blotted.
DetailsParticles extracted from dopaminergic varicosities

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 459
ExtractionNumber tomograms: 59 / Number images used: 9249 / Method: 3D classification and manual curation / Software - Name: Warp (ver. 1.09) / Details: 2 rounds
CTF correctionSoftware - Name: Warp (ver. 1.09) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1 / Avg.num./class: 2000 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)

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Atomic model buiding 1

Initial modelPDB ID:

7lup


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT

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