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- EMDB-47080: Sub-tomogram average of the V-ATPase from isolated lysosomes -

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Basic information

Entry
Database: EMDB / ID: EMD-47080
TitleSub-tomogram average of the V-ATPase from isolated lysosomes
Map data
Sample
  • Complex: Structure of the V-ATPase from isolated lysosomes
KeywordsProton pump / ATP hydrolysis / native lysosomal membrane / V-ATPase / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 24.3 Å
AuthorsDe Jesus-Perez JJ / Mcveigh B / Mihelc EM / Moiseenkova-Bell VY
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144120 United States
CitationJournal: Nat Commun / Year: 2025
Title: Visualization of lysosomal membrane proteins by cryo electron tomography.
Authors: Bridget M McVeigh / José J De Jesús-Pérez / Dirk H Siepe / Prerana Gogoi / Shrawan Kumar Mageswaran / Marian Kalocsay / Elaine M Mihelc / Vera Y Moiseenkova-Bell /
Abstract: Lysosomes are essential organelles for cellular homeostasis and signaling, with dysfunction linked to neurological disorders, lysosomal storage diseases, and cancer. While proteomics has advanced our ...Lysosomes are essential organelles for cellular homeostasis and signaling, with dysfunction linked to neurological disorders, lysosomal storage diseases, and cancer. While proteomics has advanced our understanding of lysosomal composition, the structural characterization of lysosomal membrane proteins in their native environment remains a significant challenge. Here, we developed a cryo electron tomography workflow to visualize lysosomal membrane proteins within intact, native lysosomal membranes. We isolated endolysosomes by independently targeting two lysosomal membrane proteins, transient receptor potential mucolipin 1 and transmembrane protein 192, enriching organelles that exhibited the expected morphology and proteomic composition of the endolysosomal system. Sub-tomogram averaging enabled the structural refinement of key membrane and membrane-associated proteins, including V-ATPase, Flotillin, and Clathrin, directly within the lysosomal membrane, revealing their heterogeneous distribution across endolysosomal organelles. By integrating proteomics with structural biology, our workflow establishes a powerful platform for studying lysosomal membrane protein function in health and disease, paving the way for future discoveries in membrane-associated lysosomal mechanisms.
History
DepositionSep 18, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47080.png

Downloads & links

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Map

FileDownload / File: emd_47080.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 360 pix.
= 608.4 Å		1.69 Å/pix.
x 360 pix.
= 608.4 Å		1.69 Å/pix.
x 360 pix.
= 608.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.012579427 - 0.030223029
Average (Standard dev.)0.00015231589 (±0.0017190306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 608.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47080_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #2

Fileemd_47080_half_map_2.map
Projections & Slices
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Sample components

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Entire : Structure of the V-ATPase from isolated lysosomes

EntireName: Structure of the V-ATPase from isolated lysosomes
Components
  • Complex: Structure of the V-ATPase from isolated lysosomes

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Supramolecule #1: Structure of the V-ATPase from isolated lysosomes

SupramoleculeName: Structure of the V-ATPase from isolated lysosomes / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 7.25
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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 / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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) / Resolution.type: BY AUTHOR / Resolution: 24.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 1325
ExtractionNumber tomograms: 617 / Number images used: 22044 / Reference model: 6wm2 / Method: template matching / Software - Name: RELION (ver. 5.0)
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 2 / Avg.num./class: 1113 / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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