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- EMDB-43049: Cryo-electron tomogram of mitochondria from cryo-FIB milled l-Opa... -

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Basic information

Entry
Database: EMDB / ID: EMD-43049
TitleCryo-electron tomogram of mitochondria from cryo-FIB milled l-Opa1* mouse embryonic fibroblasts
Map data
Sample
  • Cell: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletion
Keywordsmitochondria / cristae / remodeler / fusogen / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsFry MY / Navarro PP / Ananda VY / Ge Y / McDonald JL / Hakim P / Lugo CM / Luce BE / Chao LH
Funding support United States, Switzerland, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142553 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK125263 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA248565 United States
Jane Coffin Childs (JCC) Fund United States
Swiss National Science FoundationP2BSP3_188112 Switzerland
Swiss National Science FoundationP400PB_199252 Switzerland
CitationJournal: EMBO J / Year: 2024
Title: In situ architecture of Opa1-dependent mitochondrial cristae remodeling.
Authors: Michelle Y Fry / Paula P Navarro / Pusparanee Hakim / Virly Y Ananda / Xingping Qin / Juan C Landoni / Sneha Rath / Zintis Inde / Camila Makhlouta Lugo / Bridget E Luce / Yifan Ge / Julie L ...Authors: Michelle Y Fry / Paula P Navarro / Pusparanee Hakim / Virly Y Ananda / Xingping Qin / Juan C Landoni / Sneha Rath / Zintis Inde / Camila Makhlouta Lugo / Bridget E Luce / Yifan Ge / Julie L McDonald / Ilzat Ali / Leillani L Ha / Benjamin P Kleinstiver / David C Chan / Kristopher A Sarosiek / Luke H Chao /
Abstract: Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms ...Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria, while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and show a compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling.
History
DepositionDec 7, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43049.png

Downloads & links

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Map

FileDownload / File: emd_43049.map.gz / Format: CCP4 / Size: 315.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
22.06 Å/pix.
x 225 pix.
= 4963.5 Å		22.06 Å/pix.
x 720 pix.
= 15883.199 Å		22.06 Å/pix.
x 511 pix.
= 11272.66 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: 22.06 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-32.206435999999997 - 87.248069999999998
Average (Standard dev.)13.352292 (±2.9149015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-104104-113
Dimensions720511225
Spacing511720225
CellA: 11272.66 Å / B: 15883.199 Å / C: 4963.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : mitochondria in mouse embryonic fibroblasts with OMA1 deletion an...

EntireName: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletion
Components
  • Cell: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletion

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Supramolecule #1: mitochondria in mouse embryonic fibroblasts with OMA1 deletion an...

SupramoleculeName: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletion
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 5 / Focused ion beam - Current: 0.01 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 88 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Aquilos2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 46

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