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- EMDB-36103: Cryo-EM map of Euglena gracilis respiratory complex I in the NADH... -

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Basic information

Entry
Database: EMDB / ID: EMD-36103
TitleCryo-EM map of Euglena gracilis respiratory complex I in the NADH state, peripheral arm focused
Map data
Sample
  • Complex: Euglena gracilis respiratory complex I, NADH state
Keywordsrespiratory complex / membrane protein / Euglena gracilis / ELECTRON TRANSPORT
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsWu MC / He ZX / Tian HT / Hu YQ / Han FZ / Zhou L
Funding support1 items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor
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
DepositionMay 3, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36103.png

Downloads & links

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Map

FileDownload / File: emd_36103.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.2486444 - 7.5051937
Average (Standard dev.)0.0061608637 (±0.16516654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36103_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_36103_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Euglena gracilis respiratory complex I, NADH state

EntireName: Euglena gracilis respiratory complex I, NADH state
Components
  • Complex: Euglena gracilis respiratory complex I, NADH state

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Supramolecule #1: Euglena gracilis respiratory complex I, NADH state

SupramoleculeName: Euglena gracilis respiratory complex I, NADH state / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 1.5 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

Concentration3.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMTrisTrimethylsilyl
200.0 mMNaClSodium chloride
1.0 mMEDTAEDTA Ethylene diamine tetraacetic acid
0.002 %PMSFPhenylmethylsulfonyl fluoride
0.001 %CHSCholesteryl hemisuccinate
0.007 %LMNGLauryl maltose neopentyl glycol

Details: SEC-Q buffer (30 mM Tris pH 7.4, 200 mM NaCl, 1mM EDTA, 0.002% PMSF (w/v), 0.001% CHS (w/v), 0.007% LMNG (w/v))
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 25mA
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: 2949 / Average exposure time: 7.0 sec. / Average electron dose: 61.5 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: 130000
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: 468732
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: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 76643
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: 1 / Avg.num./class: 76643 / 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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