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- EMDB-36109: Cryo-EM composite map of Euglena gracilis complex I, NADH state -
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Open data
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Basic information
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Title | Cryo-EM composite map of Euglena gracilis complex I, NADH state | |||||||||
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![]() | Electron transport chain / respiratory complex / membrane protein / Euglena gracilis / ELECTRON TRANSPORT | |||||||||
Function / homology | ![]() respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / mitochondrial membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
![]() | Wu MC / He ZX / Tian HT / Hu YQ / Han FZ / Zhou L | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 373.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 82.2 KB 82.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 104 KB | ||
Filedesc metadata | ![]() | 18.7 KB | ||
Others | ![]() ![]() | 391 MB 390.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j9jMC ![]() 8iufC ![]() 8iujC ![]() 8j9hC ![]() 8j9iC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36109_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36109_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Euglena gracilis respiratory complex I, NADH state
+Supramolecule #1: Euglena gracilis respiratory complex I, NADH state
+Macromolecule #1: NDUFS1A
+Macromolecule #2: NDUFS1B
+Macromolecule #3: ND2B
+Macromolecule #4: ND4L
+Macromolecule #5: NDUFA1
+Macromolecule #6: NDUFA2
+Macromolecule #7: NDUFA3
+Macromolecule #8: NDUFA5
+Macromolecule #9: NDUFA6
+Macromolecule #10: NDUFA7
+Macromolecule #11: NDUFA8
+Macromolecule #12: NDUFA9
+Macromolecule #13: NDUFAB1-alpha
+Macromolecule #14: NDUFAB1-beta
+Macromolecule #15: NDUFA12
+Macromolecule #16: NDUFA13
+Macromolecule #17: NDUFA11
+Macromolecule #18: NDUFB2
+Macromolecule #19: NDUFB3
+Macromolecule #20: NDUFB4
+Macromolecule #21: NDUFB5
+Macromolecule #22: NDUFB6
+Macromolecule #23: NDUFB7
+Macromolecule #24: NDUFB8
+Macromolecule #25: NDUFB9
+Macromolecule #26: NDUFB10
+Macromolecule #27: NDUFB11
+Macromolecule #28: NDUFC2
+Macromolecule #29: NDUEG1
+Macromolecule #30: NDUEG2
+Macromolecule #31: NDUEG3
+Macromolecule #32: NDUEG4
+Macromolecule #33: NDUEG5
+Macromolecule #34: NDUEG6
+Macromolecule #35: NDUEG8
+Macromolecule #36: NDUEG10
+Macromolecule #37: NDUEG11
+Macromolecule #38: NDUEG12
+Macromolecule #39: NDUEG13
+Macromolecule #40: NDUFX
+Macromolecule #41: NDUCA1
+Macromolecule #42: NDUCA2
+Macromolecule #43: NDUCA3
+Macromolecule #44: ND1
+Macromolecule #45: ND2A
+Macromolecule #46: ND3
+Macromolecule #47: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #48: ND5
+Macromolecule #49: NDUFS2
+Macromolecule #50: NDUFS3
+Macromolecule #51: NDUFS4
+Macromolecule #52: NDUFS5
+Macromolecule #53: NDUFS6
+Macromolecule #54: NDUFS7
+Macromolecule #55: NDUFS8
+Macromolecule #56: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
+Macromolecule #57: NDUFV1
+Macromolecule #58: NDUFV2
+Macromolecule #59: NDUEG7
+Macromolecule #60: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #61: IRON/SULFUR CLUSTER
+Macromolecule #62: POTASSIUM ION
+Macromolecule #63: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #64: CARDIOLIPIN
+Macromolecule #65: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #66: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #67: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #68: UBIQUINONE-10
+Macromolecule #69: ZINC ION
+Macromolecule #70: FLAVIN MONONUCLEOTIDE
+Macromolecule #71: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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)) | |||||||||||||||||||||
Grid | Model: 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 | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8j9j: |