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- EMDB-34405: Cryo-EM structure of Tetrahymena thermophila respiratory super-co... -

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Basic information

Entry
Database: EMDB / ID: EMD-34405
TitleCryo-EM structure of Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II, copy2
Map data
Sample
  • Complex: Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II
KeywordsElectron transport chain / supercomplex / membrane protein / Tetrahymena thermophila / ELECTRON TRANSPORT
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.77 Å
AuthorsZhou L
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2023
Title: Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae.
Authors: Fangzhu Han / Yiqi Hu / Mengchen Wu / Zhaoxiang He / Hongtao Tian / Long Zhou /
Abstract: Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein ...Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein complexes (I-IV). Here we report cryo-EM structures of its ~8 MDa megacomplex IV+ (I + III+ II), as well as a ~ 10.6 MDa megacomplex (IV + I + III+ II) at lower resolution. In megacomplex IV+ (I + III+ II), each CIV protomer associates one copy of supercomplex I + III and one copy of CII, forming a half ring-shaped architecture that adapts to the membrane curvature of mitochondrial cristae. Megacomplex (IV+ I + III+ II) defines the relative position between neighbouring half rings and maintains the proximity between CIV and CIII cytochrome c binding sites. Our findings expand the current understanding of divergence in eukaryotic electron transport chain organization and how it is related to mitochondrial morphology.
History
DepositionSep 27, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34405.png

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Map

FileDownload / File: emd_34405.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.3103861 - 0.5007485
Average (Standard dev.)0.000628629 (±0.023055576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 840.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34405_half_map_1.map
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Half map: #2

Fileemd_34405_half_map_2.map
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Sample components

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Entire : Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II

EntireName: Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II
Components
  • Complex: Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II

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Supramolecule #1: Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II

SupramoleculeName: Tetrahymena thermophila respiratory super-complex SC IV2+I+III2+II
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB210

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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

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTrimethylsilyl
50.0 mMNaClSodium chloride
0.002 %PMSFPhenylmethylsulfonyl fluoride
0.1 %Digidigitonin

Details: SEC buffer (20 mM Tris pH 7.4, 50 mM NaCl, 0.002% PMSF, 0.1% digitonin (w/v))
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11182 / Average exposure time: 8.46 sec. / Average electron dose: 51.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 707844
Startup modelType of model: INSILICO MODEL
In silico model: 3D ab-inito model reconstruction in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 19023
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. v3.3.2)
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. v3.3.2)
Final 3D classificationNumber classes: 200 / Avg.num./class: 3538
FSC plot (resolution estimation)

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