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- EMDB-71865: Octacalcium phosphate-like precipitates -

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Basic information

Entry
Database: EMDB / ID: EMD-71865
TitleOctacalcium phosphate-like precipitates
Map dataOctacalcium phosphate-like precipitates
Sample
  • Cell: Octacalcium phosphate-like precipitates
KeywordsCalcium-phosphate / sheet / UNKNOWN FUNCTION
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsAnderson EA / Ludtke SJ
Funding support United States, 6 items
OrganizationGrant numberCountry
Beckman Foundation2021FIB-41
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS132517 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM151999 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS062829 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH137505 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS101686 United States
CitationJournal: Mol Brain / Year: 2026
Title: Primary cortical neurons precipitate and extrude large mitochondria-associated calcium-phosphate sheets with a bone-precursor-like ultrastructure.
Authors: Erik D Anderson / Christopher A Cronkite / Philip R Baldwin / Carlota P Abella / Joseph G Duman / Ashleigh N Simmonds / M Neal Waxham / Kimberley F Tolias / Steven J Ludtke /
Abstract: Calcium-phosphate (CaP) is a ubiquitous inorganic compound that plays an important structural role in healthy bone and teeth formation, but its pathologic buildup can occur in dyshomeostatic calcium ...Calcium-phosphate (CaP) is a ubiquitous inorganic compound that plays an important structural role in healthy bone and teeth formation, but its pathologic buildup can occur in dyshomeostatic calcium disorders like Alzheimer's disease and Leigh syndrome. The nexus of pathologic extracellular CaP in the nervous system is not well understood, but prior evidence suggests mitochondria could be a source. We have observed mitochondria-sized sheet-like CaP aggregates within functional wild type cortical neuron cultures at 1 and 20 days in vitro. Neurons were extracted from embryonic day 18 (E18) rat embryos following standard protocols to study neuronal structure and function. We have used a combination of cryo-ET, cryo-CLEM, and LDSAED to demonstrate that these aggregates are octacalcium phosphate-like, are associated with mitochondria, and that at least a portion are extruded via migrasomes. Visually similar aggregates were previously observed in Huntington's disease model neurons, but in that study they were not observed in WT controls. These findings show that this CaP aggregation process occurs routinely in WT neurons and may reveal an important link for how mitochondria may participate in calcification, highlighting them as potential therapeutic targets in neurological disorders characterized by pathological calcification, such as Alzheimer's disease.
History
DepositionJul 30, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71865.png

Downloads & links

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Map

FileReleased
AnnotationOctacalcium phosphate-like precipitates
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.82 Å/pix.
x 512 pix.
= 6566.207 Å		12.82 Å/pix.
x 1024 pix.
= 13132.413 Å		12.82 Å/pix.
x 1024 pix.
= 13132.413 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: 12.82462 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-36.551994000000001 - 26.003437000000002
Average (Standard dev.)-0.5226275 (±4.0836887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-512-512-256
Dimensions10241024512
Spacing10241024512
CellA: 13132.413 Å / B: 13132.413 Å / C: 6566.2065 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Octacalcium phosphate-like precipitates

EntireName: Octacalcium phosphate-like precipitates
Components
  • Cell: Octacalcium phosphate-like precipitates

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Supramolecule #1: Octacalcium phosphate-like precipitates

SupramoleculeName: Octacalcium phosphate-like precipitates / type: cell / 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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Instrument: LEICA EM GP
DetailsE18 rat cortical neurons grown on holey-carbon grids for 20 days in neurobasal media with glutamine and B27
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 2.0 µm

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Image processing

DetailsTomogram was reconstructed with EMAN2 as described previously: Chen, M., J.M. Bell, X. Shi, S.Y. Sun, Z. Wang, and S.J. Ludtke. 2019. A complete data processing workflow for cryo-ET and subtomogram averaging. Nat Methods. 16:1161?1168. doi:10.1038/s41592-019-0591-8.
Final reconstructionSoftware - Name: EMAN2 / Number images used: 45
CTF correctionSoftware - Name: EMAN2 / Details: Tomogram was CTF corrected with EMAN2 / Type: PHASE FLIPPING ONLY

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