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Yorodumi- EMDB-16518: Cryo-EM structure NDUFS4 knockout complex I from Mus musculus hea... -
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Basic information
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| Title | Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 3). | ||||||||||||
Map data | globally sharpened map | ||||||||||||
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Keywords | NADH ubiquinone oxidoreductase / Complex I / OXIDOREDUCTASE | ||||||||||||
| Function / homology | Function and homology informationnegative regulation of insulin secretion involved in cellular response to glucose stimulus / Mitochondrial protein import / blastocyst hatching / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / Respiratory electron transport ...negative regulation of insulin secretion involved in cellular response to glucose stimulus / Mitochondrial protein import / blastocyst hatching / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / Respiratory electron transport / protein insertion into mitochondrial inner membrane / response to light intensity / iron-sulfur cluster assembly complex / sperm head-tail coupling apparatus / Mitochondrial protein degradation / mitochondrial large ribosomal subunit assembly / mitochondrial ATP synthesis coupled electron transport / protein lipoylation / cellular response to oxygen levels / respiratory chain complex / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / ubiquinone biosynthetic process / neural precursor cell proliferation / gliogenesis / negative regulation of non-canonical NF-kappaB signal transduction / response to hydroperoxide / cardiac muscle tissue development / cellular respiration / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / oxygen sensor activity / sperm principal piece / cellular response to glucocorticoid stimulus / iron-sulfur cluster assembly / NADH:ubiquinone reductase (H+-translocating) / sperm end piece / ubiquinone binding / mitochondrial electron transport, NADH to ubiquinone / positive regulation of ATP biosynthetic process / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / reactive oxygen species metabolic process / cerebellum development / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / positive regulation of execution phase of apoptosis / quinone binding / extrinsic apoptotic signaling pathway / cellular response to interferon-beta / neurogenesis / cellular response to retinoic acid / ATP synthesis coupled electron transport / cilium assembly / negative regulation of reactive oxygen species biosynthetic process / Neutrophil degranulation / response to hormone / in utero embryonic development / ionotropic glutamate receptor binding / sperm midpiece / acrosomal vesicle / iron-sulfur cluster binding / aerobic respiration / response to cocaine / monooxygenase activity / response to hydrogen peroxide / respiratory electron transport chain / response to nicotine / synaptic membrane / circadian rhythm / myelin sheath / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / mitochondrial membrane / positive regulation of protein catabolic process / FMN binding / 4 iron, 4 sulfur cluster binding / nervous system development / protease binding / response to oxidative stress / response to hypoxia / response to ethanol / nuclear body / electron transfer activity / nuclear speck / mitochondrial inner membrane / response to xenobiotic stimulus / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / neuronal cell body / dendrite / protein kinase binding / synapse / protein-containing complex binding Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Yin Z / Bridges HR / Agip ANA / Hirst J | ||||||||||||
| Funding support | United Kingdom, 3 items
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Citation | Journal: EMBO J / Year: 2024Title: Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 mouse. Authors: Zhan Yin / Ahmed-Noor A Agip / Hannah R Bridges / Judy Hirst / ![]() Abstract: Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh ...Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, the ndufs4 mouse, to define the structural, biochemical, and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of the complex I from ndufs4 mouse hearts revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12, which replaces its paralogue NDUFAF2 in mature complex I, is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free enzyme. We propose that NDUFAF2 recruits the NADH-dehydrogenase module during assembly of the complex. Taken together, the findings provide new molecular-level understanding of the ndufs4 mouse model and complex I-linked mitochondrial disease. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_16518.map.gz | 322.6 MB | EMDB map data format | |
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| Header (meta data) | emd-16518-v30.xml emd-16518.xml | 69.3 KB 69.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_16518_fsc.xml | 15.9 KB | Display | FSC data file |
| Images | emd_16518.png | 132 KB | ||
| Masks | emd_16518_msk_1.map | 347.6 MB | Mask map | |
| Filedesc metadata | emd-16518.cif.gz | 14.6 KB | ||
| Others | emd_16518_half_map_1.map.gz emd_16518_half_map_2.map.gz | 322.2 MB 322.2 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-16518 ftp://data.pdbj.org/pub/emdb/structures/EMD-16518 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ca5MC ![]() 8c2sC ![]() 8ca1C ![]() 8ca3C ![]() 8ca4C M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_16518.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | globally sharpened map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.352 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_16518_msk_1.map | ||||||||||||
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| Density Histograms |
-Half map: half map 1
| File | emd_16518_half_map_1.map | ||||||||||||
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| Annotation | half map 1 | ||||||||||||
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| Density Histograms |
-Half map: half map 2
| File | emd_16518_half_map_2.map | ||||||||||||
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| Annotation | half map 2 | ||||||||||||
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Sample components
+Entire : Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
+Supramolecule #1: Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
+Macromolecule #1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 2
+Macromolecule #2: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #15: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #19: Acyl carrier protein, mitochondrial
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #23: MCG5603
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #42: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #43: IRON/SULFUR CLUSTER
+Macromolecule #44: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #45: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #46: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #47: FLAVIN MONONUCLEOTIDE
+Macromolecule #48: Ubiquinone-9
+Macromolecule #49: CARDIOLIPIN
+Macromolecule #50: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #51: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #53: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 3.82 mg/mL | |||||||||||||||
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| Buffer | pH: 7.14 Component:
Details: pH was corrected at room temperature ~22 C | |||||||||||||||
| Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United Kingdom, 3 items
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Processing
FIELD EMISSION GUN

