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- EMDB-35667: Cryo-EM map of Euglena gracilis supercomplex III2+IV2, complex II... -

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Basic information

Entry
Database: EMDB / ID: EMD-35667
TitleCryo-EM map of Euglena gracilis supercomplex III2+IV2, complex III2 focused
Map data
Sample
  • Complex: Euglena gracilis supercomplex III2+IV2
KeywordsElectron transport chain / supercomplex / membrane protein / Euglena gracilis / ELECTRON TRANSPORT
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWu MC / He ZX / Tian HT / Hu YQ / Zhou L
Funding support China, 1 items
OrganizationGrant numberCountry
Zhejiang UniversityZJU100 Young Professor China
CitationJournal: Nat Commun / Year: 2024
Title: Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism.
Authors: Zhaoxiang He / Mengchen Wu / Hongtao Tian / Liangdong Wang / Yiqi Hu / Fangzhu Han / Jiancang Zhou / Yong Wang / Long Zhou /
Abstract: Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron ...Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III + IV and supercomplex III + IV. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
History
DepositionMar 16, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35667.png

Downloads & links

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Map

FileDownload / File: emd_35667.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 448 pix.
= 537.6 Å		1.2 Å/pix.
x 448 pix.
= 537.6 Å		1.2 Å/pix.
x 448 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-4.3821425 - 8.312004999999999
Average (Standard dev.)0.004628295 (±0.21199031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 537.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35667_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35667_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 : Euglena gracilis supercomplex III2+IV2

EntireName: Euglena gracilis supercomplex III2+IV2
Components
  • Complex: Euglena gracilis supercomplex III2+IV2

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Supramolecule #1: Euglena gracilis supercomplex III2+IV2

SupramoleculeName: Euglena gracilis supercomplex III2+IV2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 1.4 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

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMTrisTrimethylsilyl
100.0 mMNaClSodium chloride
0.002 %PMSFPhenylmethylsulfonyl fluoride
0.1 %GDNGlyco-diosgenin
1.0 mMEDTAEthylene diamine tetraacetic acid

Details: SEC buffer (30 mM Tris pH 7.4, 100 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v), 1mM EDTA)
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: 15mA
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: 9807 / Average exposure time: 7.8 sec. / Average electron dose: 51.51 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: 1.8 µm / Nominal defocus min: 0.6 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: 3232325
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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 135598
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: 4 / Avg.num./class: 45074 / Software - Name: cryoSPARC (ver. v3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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