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- PDB-7a24: Assembly intermediate of the plant mitochondrial complex I -

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Basic information

Entry
Database: PDB / ID: 7a24
TitleAssembly intermediate of the plant mitochondrial complex I
Components
  • 13kDa
  • 15kDa
  • 18kDa
  • 24kDa
  • 39kDa
  • 51kDa
  • 75kDa
  • ACPM1
  • B13
  • B14
  • B14.5a
  • B14.5b
  • B16.6
  • B17.2
  • B8
  • B9
  • CA1
  • CAL1
  • GLDH
  • MNLL
  • MWFE
  • Nad1m
  • Nad2m
  • Nad3m
  • Nad4Lm
  • Nad6m
  • Nad7m
  • Nad9m
  • P2
  • PGIV
  • PSST
  • TYKY
  • Unk1
KeywordsMEMBRANE PROTEIN / Respiration / Complex I / mitochondria / plant
Function / homology
Function and homology information


galactonolactone dehydrogenase activity / L-galactonolactone dehydrogenase / L-gulono-1,4-lactone dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase complex / L-ascorbic acid biosynthetic process / cold acclimation / D-arabinono-1,4-lactone oxidase activity / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases ...galactonolactone dehydrogenase activity / L-galactonolactone dehydrogenase / L-gulono-1,4-lactone dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase complex / L-ascorbic acid biosynthetic process / cold acclimation / D-arabinono-1,4-lactone oxidase activity / 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
D-arabinono-1,4-lactone oxidase / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / 4Fe-4S ferredoxin, iron-sulphur binding, 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, 30kDa subunit, conserved site ...D-arabinono-1,4-lactone oxidase / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / 4Fe-4S ferredoxin, iron-sulphur binding, 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, 30kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NAD(P)H-quinone oxidoreductase subunit D/H / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / [NiFe]-hydrogenase, large subunit / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / FAD-binding, type PCMH-like superfamily / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / Trimeric LpxA-like superfamily / Galactonolactone dehydrogenase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NAD(P)-binding domain / FAD-binding domain, PCMH-type / FAD-binding, type PCMH, subdomain 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Phosphopantetheine binding ACP domain / NAD(P)H-binding / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / ETC complex I subunit conserved region / Zinc-finger domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase / NADH-ubiquinone oxidoreductase MWFE subunit / CHCH domain / GRIM-19 protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / Phosphopantetheine attachment site / Bacterial transferase hexapeptide (six repeats) / FAD binding domain / Proton-conducting membrane transporter / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / 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 / SLBB domain / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / Molybdopterin oxidoreductase / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 4Fe-4S dicluster domain / NADH ubiquinone oxidoreductase, 20 Kd subunit / GRIM-19 / FAD-binding, type PCMH, subdomain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, 30kDa subunit / Hexapeptide repeat / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / Ribosomal protein/NADH dehydrogenase domain / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH-quinone oxidoreductase subunit E-like / Acyl carrier protein (ACP) / FAD linked oxidase, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit
Gamma carbonic anhydrase-like 1, mitochondrial / Uncharacterized protein At2g27730, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4L ...Gamma carbonic anhydrase-like 1, mitochondrial / Uncharacterized protein At2g27730, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / At4g16450 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / At2g46540/F11C10.23 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Furry / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / L-galactono-1,4-lactone dehydrogenase, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
Biological speciesBrassica oleracea (wild cabbage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSoufari, H. / Waltz, F. / Hashem, Y.
Funding support France, 2items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: 51kDa
I: Nad2m
J: Nad3m
N: Nad6m
H: Nad1m
K: Nad4Lm
Y: PGIV
Z: B16.6
V: MWFE
W: B9
S: B14.5a
i: B14.5b
j: 15kDa
G: Nad7m
C: 75kDa
T: 39kDa
F: Nad9m
B: 24kDa
O: 18kDa
P: 13kDa
R: B13
U: B17.2
E: PSST
D: TYKY
X: B14
c: MNLL
Q: B8
k: ACPM1
r: Unk1
n: P2
o: CAL1
q: CA1
p: CA1
z: GLDH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)837,56551
Polymers829,75234
Non-polymers7,81317
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 32 types, 33 molecules AIJNHKYZVWSijGCTFBOPRUEDXcQkno...

#1: Protein 51kDa


Mass: 53522.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FNN5*PLUS
#2: Protein Nad2m


Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O05000*PLUS
#3: Protein Nad3m


Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P92533*PLUS
#4: Protein Nad6m


Mass: 23700.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P60497*PLUS
#5: Protein Nad1m


Mass: 36049.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P92558*PLUS
#6: Protein Nad4Lm


Mass: 11139.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q04614*PLUS
#7: Protein PGIV


Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8LGE7*PLUS
#8: Protein B16.6


Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8RWA7*PLUS
#9: Protein MWFE


Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9C9Z5*PLUS
#10: Protein B9


Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9ZPY5*PLUS
#11: Protein B14.5a


Mass: 15060.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SD78*PLUS
#12: Protein B14.5b


Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q94AL6*PLUS
#13: Protein 15kDa


Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9LZI6*PLUS
#14: Protein Nad7m


Mass: 45020.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P93306*PLUS
#15: Protein 75kDa


Mass: 81619.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FGI6*PLUS
#16: Protein 39kDa


Mass: 43988.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SK66*PLUS
#17: Protein Nad9m


Mass: 22910.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q95748*PLUS
#18: Protein 24kDa


Mass: 28423.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O22769*PLUS
#19: Protein 18kDa


Mass: 17160.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FJW4*PLUS
#20: Protein 13kDa


Mass: 12251.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9M6*PLUS
#21: Protein B13


Mass: 19201.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FLX7*PLUS
#22: Protein B17.2


Mass: 18346.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9M9*PLUS
#23: Protein PSST


Mass: 24071.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q42577*PLUS
#24: Protein TYKY


Mass: 25410.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FX83*PLUS
#25: Protein B14


Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9LHI0*PLUS
#26: Protein MNLL


Mass: 11355.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q84W12*PLUS
#27: Protein B8


Mass: 10865.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FIJ2*PLUS
#28: Protein ACPM1


Mass: 13735.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P53665*PLUS
#30: Protein P2


Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9ZUX4*PLUS
#31: Protein CAL1


Mass: 27599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FMV1*PLUS
#32: Protein CA1


Mass: 30010.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FWR5*PLUS
#33: Protein GLDH


Mass: 68652.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SU56*PLUS

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Protein/peptide , 1 types, 1 molecules r

#29: Protein/peptide Unk1


Mass: 1723.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)

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Non-polymers , 9 types, 17 molecules

#34: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#35: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#36: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H83O13P
#37: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#38: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#39: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#40: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#41: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#42: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plant mitochondrial respiratory complex I assembly intermediate in presence of GLDH
Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Organ: Flower / Organelle: Mitochondria
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
13RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36513 / Symmetry type: POINT

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