- PDB-8j9h: Cryo-EM structure of Euglena gracilis respiratory complex I, deac... -
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Basic information
Entry
Database: PDB / ID: 8j9h
Title
Cryo-EM structure of Euglena gracilis respiratory complex I, deactive state
Components
NADH dehydrogenase subunit 5
NADH-ubiquinone oxidoreductase chain 4
ND1
ND2A
ND3
ND4L
ND5
NDUCA1
NDUCA2
NDUCA3
NDUEG1
NDUEG10
NDUEG11
NDUEG12
NDUEG13
NDUEG2
NDUEG3
NDUEG4
NDUEG5
NDUEG6
NDUEG7
NDUEG8
NDUFA1
NDUFA11
NDUFA12
NDUFA13
NDUFA2
NDUFA3
NDUFA5
NDUFA6
NDUFA7
NDUFA8
NDUFA9
NDUFAB1-alpha
NDUFAB1-beta
NDUFB10
NDUFB11
NDUFB2
NDUFB3
NDUFB4
NDUFB5
NDUFB6
NDUFB7
NDUFB8
NDUFB9
NDUFC2
NDUFS2
NDUFS3
NDUFS4
NDUFS5
NDUFS6
NDUFS7
NDUFS8
NDUFV1
NDUFV2
NDUFX
NDUS1A
NDUS1B
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
Keywords
ELECTRON TRANSPORT / Electron transport chain / complex / membrane protein / Euglena gracilis
Function / homology
Function and homology information
respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane Similarity search - Function
Journal: 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.
Average exposure time: 7 sec. / Electron dose: 61.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2702
Image scans
Width: 4096 / Height: 4096
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Processing
EM software
ID
Name
Version
Category
1
crYOLO
1.6.0
particleselection
2
EPU
imageacquisition
4
CTFFIND
4.1
CTFcorrection
7
PHENIX
1.20.1
modelfitting
8
Coot
0.9.6
modelfitting
10
cryoSPARC
v3.3.2
initialEulerassignment
11
cryoSPARC
v3.3.2
finalEulerassignment
12
cryoSPARC
v3.3.2
classification
13
cryoSPARC
v3.3.2
3Dreconstruction
14
PHENIX
1.20.1
modelrefinement
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 460135
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68660 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
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