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- EMDB-11513: Focused reconstruction of the plant mitochondrial complex I -

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Basic information

Entry
Database: EMDB / ID: EMD-11513
TitleFocused reconstruction of the plant mitochondrial complex I
Map data
SampleMitochondrial respiratory complex I
Function / homology
Function and homology information


L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase complex / L-ascorbic acid biosynthetic process / D-arabinono-1,4-lactone oxidase activity / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases ...L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase complex / L-ascorbic acid biosynthetic process / D-arabinono-1,4-lactone oxidase activity / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / embryo development ending in seed dormancy / photorespiration / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / acyl binding / acyl carrier activity / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / electron transport chain / NADH dehydrogenase (ubiquinone) activity / plastid / vacuolar membrane / vacuole / cobalt ion binding / quinone binding / protein homotrimerization / aerobic respiration / response to osmotic stress / respirasome / respiratory electron transport chain / mitochondrial membrane / chloroplast / FAD binding / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / mitochondrial intermembrane space / carbonate dehydratase activity / peroxisome / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / copper ion binding / oxidation-reduction process / mitochondrial matrix / electron transfer activity / nucleolus / mitochondrion / zinc ion binding / integral component of membrane / extracellular region / plasma membrane / metal ion binding / nucleus / cytosol
Phosphopantetheine binding ACP domain / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / D-arabinono-1,4-lactone oxidase / Ribosomal protein/NADH dehydrogenase domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / GRIM-19 / Galactonolactone dehydrogenase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / NADH dehydrogenase, subunit C / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial ...Phosphopantetheine binding ACP domain / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / D-arabinono-1,4-lactone oxidase / Ribosomal protein/NADH dehydrogenase domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / GRIM-19 / Galactonolactone dehydrogenase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / NADH dehydrogenase, subunit C / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, subunit G / CHCH / Trimeric LpxA-like superfamily / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Molybdopterin oxidoreductase, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NAD(P)-binding domain / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / FAD linked oxidase, N-terminal / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / Molybdopterin oxidoreductase / Hexapeptide repeat / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / FAD-binding domain, PCMH-type / Phosphopantetheine attachment site / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / FAD-binding, type PCMH-like superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NuoE domain / [NiFe]-hydrogenase, large subunit / NAD(P)H-quinone oxidoreductase subunit D/H / FAD-binding, type PCMH, subdomain 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD-binding, type PCMH, subdomain 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase, 20 Kd subunit
At2g46540/F11C10.23 / L-galactono-1,4-lactone dehydrogenase, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Furry / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial ...At2g46540/F11C10.23 / L-galactono-1,4-lactone dehydrogenase, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Furry / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase-like 1, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / At4g16450 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / Acyl carrier protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase chain 2 / Uncharacterized protein At2g27730, mitochondrial
Biological speciesBrassica oleracea (wild cabbage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSoufari H / Waltz F / Hashem Y
Funding support France, 2 items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0024-02 France
European Research Council (ERC)759120
CitationJournal: Nat Commun / Year: 2020
Title: Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM.
Authors: Heddy Soufari / Camila Parrot / Lauriane Kuhn / Florent Waltz / Yaser Hashem /
Abstract: Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the ...Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P to the P module.
History
DepositionJul 29, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11513.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 360 pix.
= 399.6 Å
1.11 Å/pix.
x 360 pix.
= 399.6 Å
1.11 Å/pix.
x 360 pix.
= 399.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.0285 / Movie #1: 0.0285
Minimum - Maximum-0.12530687 - 0.37434265
Average (Standard dev.)-0.00012703023 (±0.0047813123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 399.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z399.600399.600399.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1250.374-0.000

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Supplemental data

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Sample components

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Entire Mitochondrial respiratory complex I

EntireName: Mitochondrial respiratory complex I / Number of components: 1

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Component #1: protein, Mitochondrial respiratory complex I

ProteinName: Mitochondrial respiratory complex I / Recombinant expression: No
SourceSpecies: Brassica oleracea (wild cabbage)
Source (natural)Organelle: Mitochondria / Organ or tissue: Flower

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 65018
3D reconstructionSoftware: RELION / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF

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