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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 / 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 ...L-galactonolactone dehydrogenase / galactonolactone dehydrogenase activity / L-gulono-1,4-lactone dehydrogenase activity / respiratory chain complex I / 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:ubiquinone reductase (H+-translocating) / electron transport coupled proton transport / mitochondrial respiratory chain complex I / acyl binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / ATP synthesis coupled electron transport / plastid / NADH dehydrogenase (ubiquinone) activity / vacuolar membrane / vacuole / cobalt ion binding / quinone binding / protein homotrimerization / response to osmotic stress / respiratory electron transport chain / respirasome / aerobic respiration / mitochondrial membrane / chloroplast / FAD binding / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / carbonate dehydratase activity / peroxisome / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / copper ion binding / response to oxidative stress / mitochondrial matrix / nucleolus / protein-containing complex binding / mitochondrion / zinc ion binding / integral component of membrane / extracellular region / plasma membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Galactonolactone dehydrogenase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / D-arabinono-1,4-lactone oxidase / D-arabinono-1,4-lactone oxidase / NAD(P)H-binding / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...Galactonolactone dehydrogenase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / D-arabinono-1,4-lactone oxidase / D-arabinono-1,4-lactone oxidase / NAD(P)H-binding / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Zinc-finger domain / Zinc finger, CHCC-type / GRIM-19 / GRIM-19 protein / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-quinone oxidoreductase, subunit D / NAD(P)-binding domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / FAD-binding, type PCMH, subdomain 1 / NADH:ubiquinone oxidoreductase, subunit G / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NuoE domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH dehydrogenase, subunit C / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / SLBB domain / NADH-quinone oxidoreductase subunit E, N-terminal / Soluble ligand binding domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 30kDa subunit / Proton-conducting membrane transporter / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / FAD binding domain / FAD linked oxidase, N-terminal / FAD-binding, type PCMH, subdomain 2 / CHCH / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / CHCH domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase, 4Fe-4S domain / 4Fe-4S dicluster domain / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit
Similarity search - Domain/homology
At2g46540/F11C10.23 / L-galactono-1,4-lactone dehydrogenase, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Furry / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / 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 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Furry / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / 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-ubiquinone oxidoreductase chain 6 / 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 dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 3 / Acyl carrier protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase chain 2 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
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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Movie viewer
Structure viewerEM map:
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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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