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- EMDB-78468: Leishmania tarentolae respiratory complex V (ATP synthase) dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-78468
TitleLeishmania tarentolae respiratory complex V (ATP synthase) dimer
Map data
Sample
  • Cell: Leishmania tarentolae mitochondria
KeywordsLeishmania tarentolae / respiratory complex V / ATP synthase / ELECTRON TRANSPORT
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiao YT / Chao L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2026
Title: Conserved and divergent mitochondrial assemblies in kinetoplastid parasites
Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M ...Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M / Lian CG / Luce BE / Mian SY / Nguyen K / Paul AS / Samuelson J / Stefely JA / Udeshi ND / Mootha VK / Aphasizheva I / Chao LH / Aphasizhev R
History
DepositionAug 4, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78468.png

Downloads & links

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Map

FileDownload / File: emd_78468.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 768 pix.
= 565.248 Å		0.74 Å/pix.
x 768 pix.
= 565.248 Å		0.74 Å/pix.
x 768 pix.
= 565.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0344
Minimum - Maximum-0.080883764 - 0.1795247
Average (Standard dev.)0.00058139424 (±0.006774662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 565.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_78468_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_78468_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_78468_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Leishmania tarentolae mitochondria

EntireName: Leishmania tarentolae mitochondria
Components
  • Cell: Leishmania tarentolae mitochondria

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Supramolecule #1: Leishmania tarentolae mitochondria

SupramoleculeName: Leishmania tarentolae mitochondria / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 4649
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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