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- PDB-7o71: Cryo-EM structure of a respiratory complex I -

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Entry
Database: PDB / ID: 7o71
TitleCryo-EM structure of a respiratory complex I
Components
  • (Acyl carrier protein ...) x 2
  • (NADH dehydrogenase ...) x 2
  • (NADH-ubiquinone oxidoreductase ...) x 8
  • NUCM protein
  • Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion proton pumping / Ubiquinone
Function / homology
Function and homology information


lipoate biosynthetic process / NADH dehydrogenase / membrane protein complex / NADH dehydrogenase complex / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly / ubiquinone binding / acyl binding ...lipoate biosynthetic process / NADH dehydrogenase / membrane protein complex / NADH dehydrogenase complex / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly / ubiquinone binding / acyl binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / catalytic complex / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / protein-containing complex binding / mitochondrion / metal ion binding / membrane
Similarity search - Function
NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / 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 / 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 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / : / 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 / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NuoE domain
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-CPL / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Phosphatidylinositol / Chem-ZMP ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-CPL / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Phosphatidylinositol / Chem-ZMP / Complex 1 LYR protein domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Thioredoxin-like protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / Uncharacterized protein / Zinc finger CHCC-type domain-containing protein / NAD-dependent epimerase/dehydratase domain-containing protein / NADH dehydrogenase 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase / ETC complex I subunit conserved region-domain-containing protein / Uncharacterized protein / Uncharacterized protein / NUWM protein / NUVM protein / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase / Subunit NUHM of protein NADH:Ubiquinone oxidoreductase / NUGM protein / NUCM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsParey, K. / Vonck, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: Sci Adv / Year: 2021
Title: High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism.
Authors: Kristian Parey / Jonathan Lasham / Deryck J Mills / Amina Djurabekova / Outi Haapanen / Etienne Galemou Yoga / Hao Xie / Werner Kühlbrandt / Vivek Sharma / Janet Vonck / Volker Zickermann /
Abstract: Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes ...Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase 78 kDa subunit
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NUCM protein
G: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
H: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
I: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
K: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
L: NADH-ubiquinone oxidoreductase chain 4L
S: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
j: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
1: NADH-ubiquinone oxidoreductase chain 1
2: NADH dehydrogenase subunit 2
3: NADH-ubiquinone oxidoreductase chain 3
4: NADH-ubiquinone oxidoreductase chain 4
5: NADH-ubiquinone oxidoreductase chain 5
6: NADH-ubiquinone oxidoreductase chain 6
g: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
D: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
E: NADH-ubiquinone oxidoreductase 40 kDa subunit
F: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
J: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
M: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
O: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)
P: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Q: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)
R: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
U: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
X: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
Y: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
Z: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
a: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
b: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
c: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
d: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
e: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
f: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
h: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
i: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
n: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
8: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
9: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,015,12491
Polymers978,84242
Non-polymers36,28249
Water29,1121616
1


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

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Components

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NADH-ubiquinone oxidoreductase ... , 8 types, 8 molecules AL13456E

#1: Protein NADH-ubiquinone oxidoreductase 78 kDa subunit / NUAM protein


Mass: 79088.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU3, NADH dehydrogenase
#8: Protein NADH-ubiquinone oxidoreductase chain 4L


Mass: 9843.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4U1, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 38389.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 14506.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 54534.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMP9, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 73768.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TF58, NADH:ubiquinone reductase (H+-translocating)
#16: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 20793.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3X7, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase 40 kDa subunit


Mass: 42765.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371BY45

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NADH dehydrogenase ... , 2 types, 2 molecules B2

#2: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 53829.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH dehydrogenase subunit 2


Mass: 53381.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, NADH:ubiquinone reductase (H+-translocating)

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Protein , 30 types, 30 molecules CGHIKSjgDFJMPRUWXYZabcdefhin89

#3: Protein NUCM protein


Mass: 52521.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU1, NADH dehydrogenase
#4: Protein Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 32389.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU0, NADH dehydrogenase
#5: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 27247.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT9, NADH dehydrogenase
#6: Protein Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 25682.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT8, NADH dehydrogenase
#7: Protein Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 23455.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#9: Protein Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 28479.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6ZY23, NADH dehydrogenase
#10: Protein Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10494.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6ZY24, NADH dehydrogenase
#17: Protein subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8992.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0
#18: Protein Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63
#20: Protein Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16657.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C5F3
#21: Protein Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 20849.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CB65
#22: Protein Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15148.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5
#24: Protein Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14778.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8
#26: Protein Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12902.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1
#27: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0
#28: Protein Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5
#29: Protein Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4
#30: Protein Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18656.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0
#31: Protein Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19772.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3H5
#32: Protein Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 17328.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8ND94
#33: Protein Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8059.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#34: Protein Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 6948.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C0F2
#35: Protein Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11039.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596
#36: Protein Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 7807.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NFX6
#37: Protein Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9621.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3
#38: Protein Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16175.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N5V2
#39: Protein Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9793.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q311
#40: Protein Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13523.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CFV9
#41: Protein Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9
#42: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0

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Acyl carrier protein ... , 2 types, 2 molecules OQ

#23: Protein Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9
#25: Protein Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21

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Non-polymers , 13 types, 1665 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#44: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#45: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#46: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#47: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#48: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#49: Chemical ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H83O13P
#50: Chemical ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#51: 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.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#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.: 1 / Source method: isolated from a natural source / Formula: Zn
#54: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#55: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1616 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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 NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: GB30
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMsodium clorideNaCl1
31 mMEDTA1
40.025 %LMNG1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Calibrated magnification: 96899 X / Nominal defocus max: -2200 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 21770
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1078960
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178960 / Symmetry type: POINT
Atomic model buildingB value: 30 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6RFR

6rfr


Accession code: 6RFR / Source name: PDB / Type: experimental model

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