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- EMDB-55740: in situ subtomogram average of the V-ATPase from dopaminergic var... -

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Basic information

Entry
Database: EMDB / ID: EMD-55740
Titlein situ subtomogram average of the V-ATPase from dopaminergic varicosities
Map datain situ subtomogram average of the V-ATPase from dopaminergic varicosities
Sample
  • Complex: V-ATPase from dopaminergic varicosities
KeywordsV-ATPase / ATPase / Vacuolar-type ATPase / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 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_55740.png

Downloads & links

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Map

FileDownload / File: emd_55740.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationin situ subtomogram average of the V-ATPase from dopaminergic varicosities
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
6.76 Å/pix.
x 56 pix.
= 378.56 Å		6.76 Å/pix.
x 56 pix.
= 378.56 Å		6.76 Å/pix.
x 56 pix.
= 378.56 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 6.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.25705165 - 1.121055
Average (Standard dev.)0.047705512 (±0.16148889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions565656
Spacing565656
CellA=B=C: 378.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half 1

Fileemd_55740_half_map_1.map
AnnotationHalf_1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2

Fileemd_55740_half_map_2.map
AnnotationHalf_2
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 : V-ATPase from dopaminergic varicosities

EntireName: V-ATPase from dopaminergic varicosities
Components
  • Complex: V-ATPase from dopaminergic varicosities

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Supramolecule #1: V-ATPase from dopaminergic varicosities

SupramoleculeName: V-ATPase 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
GridModel: Quantifoil R2/2 / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Backside blotted.

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 519
ExtractionNumber tomograms: 59 / Number images used: 39300 / 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: 7 / Avg.num./class: 100 / 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:

6xbw


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

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