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- EMDB-49874: CryoET tomogram of hESC-derived retinal ganglion cell treated wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-49874
TitleCryoET tomogram of hESC-derived retinal ganglion cell treated with calcification media
Map datahESC-derived retinal ganglion cell treated with a calcification media.
Sample
  • Cell: Human retinal ganglion cell differentiated from human embryonic stem cell and treated with calcification media.
Keywordsmitochondria / cristae / granules / UNKNOWN FUNCTION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsHou C / Wu GH / Patel HR / Liao YJ / Chiu W
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2025
Title: Cryogenic electron tomography and elemental analysis of mitochondrial granules in human retinal ganglion cells.
Authors: Gong-Her Wu / Cathy Hou / Andrew Thron / Hirenkumar Rajendra Patel / Liam Spillane / Sanket Rajan Gupte / Serena Yeung-Levy / Sahil Gulati / Christopher Booth / Yaping Joyce Liao / Wah Chiu /
Abstract: Combining three-dimensional (3D) visualization with elemental analysis of vitrified cells can provide crucial insights into subcellular structures and elemental compositions in their native ...Combining three-dimensional (3D) visualization with elemental analysis of vitrified cells can provide crucial insights into subcellular structures and elemental compositions in their native environments. We present a coordinated approach using cryogenic electron energy loss spectroscopy (cryoEELS) and cryogenic electron tomography (cryoET) to characterize the elemental distribution and ultrastructure of vitrified cells. We applied this method to examine calcium disposition in the mitochondria of cultured human retinal ganglion cells (RGCs) exposed to pro-calcifying conditions relevant to optic disc drusen pathology. Our cryoEELS analysis revealed mitochondrial granules with elevated calcium signals, offering direct evidence of mitochondrial calcification. Additionally, cryoET coupled with artificial intelligence-based analysis enabled quantification of the volume and spatial distribution of these calcium granules. This integrated workflow can be broadly applied to various cell types, facilitating the study of ultrastructure and elemental distribution in subcellular structures under diverse physiological and pathological conditions, as well as in response to therapeutic interventions.
History
DepositionMar 21, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49874.png

Downloads & links

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Map

FileDownload / File: emd_49874.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhESC-derived retinal ganglion cell treated with a calcification media.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.76 Å/pix.
x 312 pix.
= 4293.12 Å		13.76 Å/pix.
x 1440 pix.
= 19814.4 Å		13.76 Å/pix.
x 1023 pix.
= 14076.48 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.76 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.0 - 3.0
Average (Standard dev.)0.0018880719 (±0.9825311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-185208-208
Dimensions14401023312
Spacing10231440312
CellA: 14076.48 Å / B: 19814.4 Å / C: 4293.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human retinal ganglion cell differentiated from human embryonic s...

EntireName: Human retinal ganglion cell differentiated from human embryonic stem cell and treated with calcification media.
Components
  • Cell: Human retinal ganglion cell differentiated from human embryonic stem cell and treated with calcification media.

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Supramolecule #1: Human retinal ganglion cell differentiated from human embryonic s...

SupramoleculeName: Human retinal ganglion cell differentiated from human embryonic stem cell and treated with calcification media.
type: cell / ID: 1 / Parent: 0 / Details: Mitochondria in situ
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.01 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 121
CTF correctionType: NONE

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