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- PDB-7a23: Plant mitochondrial respiratory complex I -

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Basic information

Entry
Database: PDB / ID: 7a23
TitlePlant mitochondrial respiratory complex I
Components
  • 13kDa
  • 15kDa
  • 18kDa
  • 20.9kDa
  • 24kDa
  • 39kDa
  • 51kDa
  • 75kDa
  • ACPM1
  • ACPM2
  • AGGG
  • B12-1
  • B13
  • B14
  • B14.5a
  • B14.5b
  • B15
  • B16.6
  • B17.2
  • B18
  • B22
  • B8
  • B9
  • CA1
  • CAL1
  • ESSS
  • MWFE
  • Nad1m
  • Nad2m
  • Nad3m
  • Nad4Lm
  • Nad4m
  • Nad5m
  • Nad6m
  • Nad7m
  • Nad9m
  • P1
  • P2
  • PDSW
  • PGIV
  • PSST
  • TYKY
  • Unk1
  • Unk2
KeywordsMEMBRANE PROTEIN / Respiration / Complex I / mitochondria / plant
Function / homology
Function and homology information


cold acclimation / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / plant-type vacuole / response to osmotic stress / plastid / cobalt ion binding / ubiquinone binding ...cold acclimation / Lyases; Carbon-oxygen lyases; Hydro-lyases / NADH dehydrogenase complex / photorespiration / embryo development ending in seed dormancy / plant-type vacuole / response to osmotic stress / plastid / cobalt ion binding / ubiquinone binding / protein homotrimerization / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / respiratory chain complex I / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / aerobic respiration / respiratory electron transport chain / proton transmembrane transport / chloroplast / carbonate dehydratase activity / mitochondrial membrane / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / NAD binding / peroxisome / FMN binding / 4 iron, 4 sulfur cluster binding / carbohydrate metabolic process / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / At2g27730-like / : / NAD(P)H-binding / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit ...NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / At2g27730-like / : / NAD(P)H-binding / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / SLBB domain / Bacterial transferase hexapeptide (six repeats) / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Trimeric LpxA-like superfamily / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / : / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / SLBB domain / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Complex 1 protein (LYR family) / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1.
Similarity search - Domain/homology
BICARBONATE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PEV / IRON/SULFUR CLUSTER / Phosphatidylinositol / UBIQUINONE-10 / NADH-ubiquinone oxidoreductase chain 2 ...BICARBONATE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PEV / IRON/SULFUR CLUSTER / Phosphatidylinositol / UBIQUINONE-10 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Acyl carrier protein 2, mitochondrial / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / At4g16450 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / 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 / Gamma carbonic anhydrase-like 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / At1g67350 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-A / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-B / Furry / At2g31490 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesBrassica oleracea (wild cabbage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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.
History
DepositionAug 15, 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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  • Deposited structure unit
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Structure viewerMolecule:
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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: 20.9kDa
Q: B8
k: ACPM1
r: Unk1
n: P2
o: CAL1
q: CA1
p: CA1
M: Nad4m
f: PDSW
g: ESSS
d: B22
a: Nad5m
b: B18
h: AGGG
e: ACPM2
l: B15
s: Unk2
m: P1
t: B12-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,005,12765
Polymers993,52245
Non-polymers11,60520
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 42 types, 43 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: P42027*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 20.9kDa


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 Nad4m


Mass: 55869.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P93313*PLUS
#34: Protein PDSW


Mass: 12555.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9B4*PLUS
#35: Protein ESSS


Mass: 12680.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8L3S7*PLUS
#36: Protein B22


Mass: 13638.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q945M1*PLUS
#37: Protein Nad5m


Mass: 74361.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P29388*PLUS
#38: Protein B18


Mass: 11757.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SKC9*PLUS
#39: Protein AGGG


Mass: 7582.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8LDK3*PLUS
#40: Protein ACPM2


Mass: 14183.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O80800*PLUS
#41: Protein B15


Mass: 8305.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SIQ8*PLUS
#43: Protein P1


Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FYF8*PLUS
#44: Protein B12-1


Mass: 8239.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9R9*PLUS

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Protein/peptide , 2 types, 2 molecules rs

#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)
#42: Protein/peptide Unk2


Mass: 1439.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)

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Non-polymers , 10 types, 20 molecules

#45: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


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


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#49: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#50: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


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


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


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


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


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: Mitochondrial respiratory complex I / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Organ: Flower / Organelle: Mitochondria
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 FIELD
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65018 / Symmetry type: POINT

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