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- EMDB-77685: ATAD3A structurally links mtDNA replication and mitochondrial fission -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-77685
TitleATAD3A structurally links mtDNA replication and mitochondrial fission
Map dataAveraged subvolumes reconstructed in relion after alignment in i3.
Sample
  • Organelle or cellular component: ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.
KeywordsmtDNA Replication / mtDNA nucleoid / Mitochondria / mitochondrial fission / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsDua N / Ma B / Oviedo S / Rahmani H / Boyd T / Park DR / Wiseman RL / Grotjahn DA
Funding support United States, 5 items
OrganizationGrant numberCountry
The Pew Charitable Trusts United States
Damon Runyon Cancer Research FoundationDRR-65-21 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS142779 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RF1NS125674 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
CitationJournal: To Be Published
Title: ATAD3A structurally links mtDNA replication and mitochondrial fission
Authors: Dua N / Ma B / Oviedo S / Rahmani H / Boyd T / Park DR / Wiseman RL / Grotjahn DA
History
DepositionJun 18, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77685.png

Downloads & links

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Map

FileDownload / File: emd_77685.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged subvolumes reconstructed in relion after alignment in i3.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 100 pix.
= 332.5 Å		3.33 Å/pix.
x 100 pix.
= 332.5 Å		3.33 Å/pix.
x 100 pix.
= 332.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.20063399 - 0.17432514
Average (Standard dev.)0.0021183765 (±0.020803038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 332.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1 created using relion reconstruct

Fileemd_77685_half_map_1.map
Annotationhalf map1 created using relion_reconstruct
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2 created using relion reconstruct

Fileemd_77685_half_map_2.map
Annotationhalf map2 created using relion_reconstruct
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.

EntireName: ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.
Components
  • Organelle or cellular component: ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.

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Supramolecule #1: ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.

SupramoleculeName: ATAD3A tether connecting IMM and OMM imaged in HeLa cell mitochondria.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R1/4 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 37 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 2 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 1861
ExtractionNumber tomograms: 25 / Number images used: 1861 / Software - Name: Warp (ver. 1.1)
CTF correctionSoftware - Name: Warp (ver. 1.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: I3
FSC plot (resolution estimation)

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