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- EMDB-32632: Cryo-EM structure of ATP synthase dimer from Tetrahymena thermophila -

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Basic information

Entry
Database: EMDB / ID: EMD-32632
TitleCryo-EM structure of ATP synthase dimer from Tetrahymena thermophila
Map dataTetrahymena thermophila complex V dimer asymmetric F1 particles
Sample
  • Complex: ATP synthase dimer
KeywordsMitochondrial respiration / electron transport chain / ATP synthase / cristae / membrane complex / ELECTRON TRANSPORT
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZhou L / Maldonado M / Padavannil A / Guo F / Letts JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM137929 United States
CitationJournal: Science / Year: 2022
Title: Structures of 's respiratory chain reveal the diversity of eukaryotic core metabolism.
Authors: Long Zhou / María Maldonado / Abhilash Padavannil / Fei Guo / James A Letts /
Abstract: Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and ...Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII (Tt-SC I+III) and a structure of Tt-CIV. Tt-SC I+III (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM8-TIM13-like domain. Our structural and functional study of the respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism.
History
DepositionJan 19, 2022-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32632.png

Downloads & links

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Map

FileDownload / File: emd_32632.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTetrahymena thermophila complex V dimer asymmetric F1 particles
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 501. Å		0.84 Å/pix.
x 600 pix.
= 501. Å		0.84 Å/pix.
x 600 pix.
= 501. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.30164137 - 0.988344
Average (Standard dev.)0.0010529055 (±0.04698757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 501.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32632_msk_1.map
Projections & Slices
AxesZYX

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Half map: Tetrahymena thermophila complex V dimer asymmetric F1 particles...

Fileemd_32632_half_map_1.map
AnnotationTetrahymena thermophila complex V dimer asymmetric F1 particles half map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Tetrahymena thermophila complex V dimer asymmetric F1 particles...

Fileemd_32632_half_map_2.map
AnnotationTetrahymena thermophila complex V dimer asymmetric F1 particles half map 2
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : ATP synthase dimer

EntireName: ATP synthase dimer
Components
  • Complex: ATP synthase dimer

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Supramolecule #1: ATP synthase dimer

SupramoleculeName: ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#58
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane
Molecular weightTheoretical: 2.0 MDa

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTris2-Amino-2-(hydroxymethyl)propane-1,3-diol
50.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
0.002 g/100 mlPMSFPhenylmethanesulfonyl fluoride

Details: Solution were made fresh from concentrated stocks, filtered and de-gassed before equilibration onto Superose6 column
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
Details: incubation time before blotting: 60s blot time: 9s blot force: 25 offset: -2 incubation after blotting: 0s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7895 / Average exposure time: 5.9 sec. / Average electron dose: 66.69 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58616 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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: 1144671
Startup modelType of model: INSILICO MODEL
In silico model: 3D ab-initio model reconstruction in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 42815
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 200 / Avg.num./class: 5723 / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

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