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- PDB-7psa: The acetogenin-bound complex I of Mus musculus resolved to 3.4 an... -

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Basic information

Entry
Database: PDB / ID: 7psa
TitleThe acetogenin-bound complex I of Mus musculus resolved to 3.4 angstroms
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsMEMBRANE PROTEIN / inhibitor-bound / detergent-solubilised / NADH:Ubiquinone oxidoreductase
Function / homology
Function and homology information


Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / : / Respiratory electron transport ...Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / : / Respiratory electron transport / protein insertion into mitochondrial inner membrane / mesenchymal stem cell differentiation / circulatory system development / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / response to light intensity / cellular response to oxygen levels / respiratory chain complex / stem cell division / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / negative regulation of non-canonical NF-kappaB signal transduction / cardiac muscle tissue development / neural precursor cell proliferation / [2Fe-2S] cluster assembly / positive regulation of mitochondrial membrane potential / adult walking behavior / cellular response to glucocorticoid stimulus / oxygen sensor activity / response to hydroperoxide / iron-sulfur cluster assembly / positive regulation of ATP biosynthetic process / adult behavior / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / NADH dehydrogenase activity / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / DNA damage response, signal transduction by p53 class mediator / NADH dehydrogenase (ubiquinone) activity / neuron development / cellular response to interferon-beta / quinone binding / ATP synthesis coupled electron transport / cellular response to retinoic acid / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / muscle contraction / tricarboxylic acid cycle / Neutrophil degranulation / cerebellum development / reactive oxygen species metabolic process / visual perception / aerobic respiration / regulation of mitochondrial membrane potential / regulation of membrane potential / respiratory electron transport chain / kidney development / fatty acid metabolic process / mitochondrion organization / neurogenesis / response to nicotine / sensory perception of sound / electron transport chain / response to cocaine / mitochondrial membrane / brain development / multicellular organism growth / : / response to hydrogen peroxide / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / cognition / circadian rhythm / positive regulation of protein catabolic process / NAD binding / fatty acid biosynthetic process / cellular senescence / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding / gene expression / neuron apoptotic process / response to ethanol / in utero embryonic development / response to oxidative stress / electron transfer activity / response to hypoxia / mitochondrial inner membrane / nuclear body / nuclear speck / mitochondrial matrix
Similarity search - Function
NmrA-like domain / NmrA-like family / Complex1_LYR-like / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase flavoprotein 3 ...NmrA-like domain / NmrA-like family / Complex1_LYR-like / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / 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] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / : / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / : / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / 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 / NDUFA6, LYR domain / Deoxynucleoside kinase domain / Deoxynucleoside kinase / 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 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / 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-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / 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 / Complex 1 LYR protein domain / 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:ubiquinone oxidoreductase, subunit G
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-88I / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER ...1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-88I / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGrba, D. / Hirst, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105663141 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: J Biol Chem / Year: 2022
Title: Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I.
Authors: Daniel N Grba / James N Blaza / Hannah R Bridges / Ahmed-Noor A Agip / Zhan Yin / Masatoshi Murai / Hideto Miyoshi / Judy Hirst /
Abstract: Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation/ubiquinone reduction to create the proton ...Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation/ubiquinone reduction to create the proton motive force used to drive ATP synthesis in oxidative phosphorylation. High-resolution single-particle electron cryo-EM analyses have provided detailed structural knowledge of the catalytic machinery of complex I, but not of the molecular principles of its energy transduction mechanism. Although ubiquinone is considered to bind in a long channel at the interface of the membrane-embedded and hydrophilic domains, with channel residues likely involved in coupling substrate reduction to proton translocation, no structures with the channel fully occupied have yet been described. Here, we report the structure (determined by cryo-EM) of mouse complex I with a tight-binding natural product acetogenin inhibitor, which resembles the native substrate, bound along the full length of the expected ubiquinone-binding channel. Our structure reveals the mode of acetogenin binding and the molecular basis for structure-activity relationships within the acetogenin family. It also shows that acetogenins are such potent inhibitors because they are highly hydrophobic molecules that contain two specific hydrophilic moieties spaced to lock into two hydrophilic regions of the otherwise hydrophobic channel. The central hydrophilic section of the channel does not favor binding of the isoprenoid chain when the native substrate is fully bound but stabilizes the ubiquinone/ubiquinol headgroup as it transits to/from the active site. Therefore, the amphipathic nature of the channel supports both tight binding of the amphipathic inhibitor and rapid exchange of the ubiquinone/ubiquinol substrate and product.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
H: NADH-ubiquinone oxidoreductase chain 1
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
O: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
T: Acyl carrier protein, mitochondrial
U: Acyl carrier protein, mitochondrial
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 subunit C2
e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
f: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
g: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
h: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
s: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,072,89280
Polymers1,046,73645
Non-polymers26,15635
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area307170 Å2
ΔGint-2165 kcal/mol
Surface area261000 Å2

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Components

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN

#1: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13251.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03899, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 36105.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18656.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03925, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03903, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68547.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03921, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51943.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03911, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 38800.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P03893, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCDIQRe

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 24715.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9DC70, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 30191.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9DCT2, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 52720.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91WD5, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit


Mass: 24068.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8K3J1, NADH:ubiquinone reductase (H+-translocating)
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / CI-18 kDa / Complex I-AQDQ / CI-AQDQ / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19814.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXZ1
#18: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 13041.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P52503
#30: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12675.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LY9

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules EFs

#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 27318.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9D6J6, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 50904.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91YT0, NADH:ubiquinone reductase (H+-translocating)
#44: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 11833.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BK30

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Protein , 2 types, 3 molecules GTU

#7: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 79866.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q91VD9, NADH:ubiquinone reductase (H+-translocating)
#20: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17390.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR21

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules OPSVWXYZabqr

#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 40657.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LC3
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 42588.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DC69
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 10932.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ75
#21: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / CI-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


Mass: 13380.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPP6
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 15311.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ5
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-19kD / CI-19kD / Complex I-PGIV / CI-PGIV / NADH-ubiquinone oxidoreductase 19 kDa subunit


Mass: 20025.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCJ5
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 15130.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8B4
#25: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic ...Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 16881.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9ERS2
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8149.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35683
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9338.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ91
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 17154.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TMF3
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12637.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1P6

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules cd

#28: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Complex I-KFYI / CI-KFYI / NADH-ubiquinone oxidoreductase KFYI subunit


Mass: 8636.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQY9
#29: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 14185.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ54

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules fghijklmnop

#31: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / CI-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6965.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0DN34
#32: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit / Neuronal protein 15.6 / p15.6


Mass: 17463.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09111
#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 21742.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQH3
#34: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15540.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3UIU2
#35: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 11982.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPU2
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / CI-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 11714.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQZ6
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / CI-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21903.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D6J5
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 15105.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC7
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 22020.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQJ8
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 16360.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR61
#41: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 21054.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCS9

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Non-polymers , 11 types, 35 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-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#49: 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.: 9 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#50: Chemical ChemComp-88I / (3~{S},5~{S})-5-methyl-3-[(13~{R})-13-oxidanyl-13-[(2~{R},5~{R})-5-[(2~{R},5~{R})-5-[(1~{R})-1-oxidanylundecyl]oxolan-2-yl]oxolan-2-yl]tridecyl]oxolan-2-one


Mass: 608.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H68O6 / Feature type: SUBJECT OF INVESTIGATION
#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.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#52: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#53: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#55: Chemical ChemComp-EHZ / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate


Mass: 584.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O9PS

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Details

Has ligand of interestY

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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 from Mus musculus
Type: COMPLEX
Details: Solubilised in DDM detergent. Native purification via anion exchange, with inhibitor acetogenin added, and size-exclusion chromatography.
Entity ID: #1-#44 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.55 / Details: pH 7.55 at 25 degrees Celsius
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HCl1
2200 mMNaCl1
30.02 w/v (%)n-Dodecyl-B-D-Maltoside1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA glow discharge. Followed by a 2-day PEGylation with a PEG-thiol reagent.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1286
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 50

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4GctfCTF correction
7Coot0.9model fittingmanual adjustments
8UCSF ChimeraX1.1model fittingrigid fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.19model refinementreal-space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 114209
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15754 / Details: Generated with a mask in RELION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6ZR2

6zr2

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