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- EMDB-44170: Artemia franciscana ATP synthase F1 domain, state 2, pH 8.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-44170
TitleArtemia franciscana ATP synthase F1 domain, state 2, pH 8.0
Map dataArtemia franciscana ATP synthase F1 domain, state 2, pH 8.0
Sample
  • Complex: Mitochondrial ATP synthase
KeywordsATP synthesis / Complex V / mitochondria / oxidative-phosphorylation / MEMBRANE PROTEIN
Biological speciesArtemia franciscana (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMnatsakanyan N / Mello JFR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG072484 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS137275 United States
CitationJournal: Cell Death Differ / Year: 2025
Title: Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.
Authors: Amrendra Kumar / Juliana da Fonseca Rezende E Mello / Yangyu Wu / Daniel Morris / Ikram Mezghani / Erin Smith / Stephane Rombauts / Peter Bossier / Juno Krahn / Fred J Sigworth / Nelli Mnatsakanyan /
Abstract: Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial ...Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial inner membranes. Ca-induced prolonged openings of mPTP under certain pathological conditions result in mitochondrial swelling and rupture of the outer membrane, leading to mitochondrial dysfunction and cell death. While the exact molecular composition and structure of mPTP remain unknown, mammalian ATP synthase was reported to form voltage and Ca-activated leak channels involved in mPT. Unlike in mammals, mitochondria of the crustacean Artemia franciscana have the ability to accumulate large amounts of Ca without undergoing the mPT. Here, we performed structural and functional analysis of A. franciscana ATP synthase to study the molecular mechanism of mPTP inhibition in this organism. We found that the channel formed by the A. franciscana ATP synthase dwells predominantly in its inactive state and is insensitive to Ca, in contrast to porcine heart ATP synthase. Single-particle cryo-electron microscopy (cryo-EM) analysis revealed distinct structural features in A. franciscana ATP synthase compared with mammals. The stronger density of the e-subunit C-terminal region and its enhanced interaction with the c-ring were found in A. franciscana ATP synthase. These data suggest an inactivation mechanism of the ATP synthase leak channel and its possible contribution to the lack of mPT in this organism.
History
DepositionMar 20, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44170.png

Downloads & links

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Map

FileDownload / File: emd_44170.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArtemia franciscana ATP synthase F1 domain, state 2, pH 8.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.361
Minimum - Maximum-2.5997717 - 4.786346
Average (Standard dev.)-0.0010817219 (±0.09616461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Artemia franciscana ATP synthase F1 domain, state 2, pH 8.0

Fileemd_44170_half_map_1.map
AnnotationArtemia franciscana ATP synthase F1 domain, state 2, pH 8.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Artemia franciscana ATP synthase F1 domain, state 2, pH 8.0

Fileemd_44170_half_map_2.map
AnnotationArtemia franciscana ATP synthase F1 domain, state 2, pH 8.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase

EntireName: Mitochondrial ATP synthase
Components
  • Complex: Mitochondrial ATP synthase

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Supramolecule #1: Mitochondrial ATP synthase

SupramoleculeName: Mitochondrial ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Artemia franciscana (crustacean)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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