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- PDB-9smg: Reduced bovine complex I in lipid nanodisc, NADH-active-altQ10 -

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Basic information

Entry
Database: PDB / ID: 9smg
TitleReduced bovine complex I in lipid nanodisc, NADH-active-altQ10
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
KeywordsELECTRON TRANSPORT / Mitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Ubiquinone / Nanodisc / NADH
Function / homology
Function and homology information


Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / Neutrophil degranulation / neural precursor cell proliferation ...Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / Neutrophil degranulation / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / Mitochondrial protein degradation / ubiquinone binding / acyl binding / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / response to cAMP / quinone binding / ATP synthesis coupled electron transport / neurogenesis / reactive oxygen species metabolic process / aerobic respiration / fatty acid binding / respiratory electron transport chain / electron transport chain / circadian rhythm / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / NAD binding / fatty acid biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / apoptotic process / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
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 ...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] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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 [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / 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: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-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 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 / 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 dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / 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 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / : / SLBB domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / 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
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / CHOLIC ACID / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / MYRISTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / CHOLIC ACID / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / MYRISTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsChung, I. / Hirst, J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
Diamond Light SourceBI22238-37 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Post-catalysis structures of mitochondrial complex I with ubiquinol-10 bound in the active site.
Authors: Injae Chung / Caroline S Pereira / John J Wright / Guilherme M Arantes / Judy Hirst /
Abstract: Respiratory complex I is a multi-subunit energy-transducing membrane enzyme essential for mitochondrial and cellular energy metabolism. It couples NADH oxidation and ubiquinone-10 (Q) reduction to ...Respiratory complex I is a multi-subunit energy-transducing membrane enzyme essential for mitochondrial and cellular energy metabolism. It couples NADH oxidation and ubiquinone-10 (Q) reduction to the concomitant pumping of four protons to generate the proton-motive force that powers oxidative phosphorylation. Despite recent advances in structural knowledge of complex I, many mechanistic aspects including the reactive binding poses of Q, how Q reduction initiates the proton transfer cascade, and how protons move through the membrane domain, remain unclear. Here, we use electron cryomicroscopy to determine structures of mammalian complex I, reconstituted into phospholipid nanodiscs containing exogenous Q and reduced by NADH, to global resolutions of 2.0 to 2.6 Å. Two conformations of a reduced QH molecule are observed, fully inserted into the Q-binding channel in the turnover-relevant closed state. By comparing the quinone species bound in oxidised and reduced complex I structures, paired with molecular dynamics simulations to investigate the charge states of key surrounding residues, we propose a series of substrate binding poses that Q transits through for reduction. Our highly hydrated structures exhibit near-continuous proton-transfer connections along the length of the membrane domain, enabling comparisons between them to assist in identifying the proton-transfer control points that are essential to catalysis.
History
DepositionSep 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: 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)1,084,235101
Polymers1,044,19645
Non-polymers40,03956
Water35,5081971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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


Mass: 13086.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: Q7JAS9, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 35716.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P03887
#10: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19110.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P03924, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10828.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P03902, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68355.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P03920, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 52158.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P03910, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39302.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P03892, 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 / PSST subunit


Mass: 23817.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P42026, 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: 30323.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P23709, 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: 52678.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Harbours a naturally occurring mutation Q129R (Q162R) in the Cambridge UK population
Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P17694, 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 / TYKY subunit


Mass: 23926.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P42028, 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: 19841.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02375
#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: 13433.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P23934
#30: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12694.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02379

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

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


Mass: 27341.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P04394, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 50718.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P25708, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#44: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 11874.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P25712

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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: 79532.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart
References: UniProt: P15690, NADH:ubiquinone reductase (H+-translocating)
#20: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17421.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P52505

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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: 39330.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Contains a naturally occurring mutation N255K (N278K) present in the Cambridge UK population
Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P34942
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 42913.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P34943
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02370
#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: 13334.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P23935
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 15083.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02366
#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: 20124.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P42029
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14666.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q8HXG6
#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-interferon-induced mortality 19 protein / GRIM-19 / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 16694.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q95KV7
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8117.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02377
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9357.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02371
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: O97725
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12590.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q05752

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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: 8796.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02376
#29: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 14143.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02827

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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: 6978.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02378
#32: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 17594.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q8HXG5
#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 21624.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02380
#34: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15444.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02367
#35: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 12298.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02374
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / CI-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 11160.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02365
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / CI-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21678.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02372
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 15206.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: P48305
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21827.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02369
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 16428.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02368
#41: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 21000.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Heart / References: UniProt: Q02373

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Non-polymers , 17 types, 2027 molecules

#45: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#46: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#51: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#52: 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
#53: 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
#54: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#55: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#56: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#58: 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
#59: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5
#60: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1971 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

-
Sample preparation

ComponentName: Mitochondrial respiratory complex I / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: heart / Organelle: Mitochondria
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMMOPS [3-(N-morpholino)propanesulfonic acid]C7H15NO4S1
250 mMPotassium chlorideKCl1
SpecimenConc.: 5.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting
Grid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Mix with NADH, then blot for 10 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: AutoStigmate and AutoComa on EPU, no AutoCTF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.14 sec. / Electron dose: 40.29 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13056
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1.0particle selection
2EPU2.12image acquisition
4RELION3.1.0CTF correction
5CTFFIND4.1CTF correction
8UCSF ChimeraX1.6.1model fitting
9UCSF ChimeraX1.7model fitting
10UCSF ChimeraX1.8model fitting
11UCSF ChimeraX1.9model fitting
12Coot0.9.6.2-premodel fitting
13PyMOL2.4.1model fitting
15RELION3.1.0initial Euler assignment
16RELION3.1.0final Euler assignment
17RELION3.1.0classification
18RELION3.13D reconstruction
19PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2721931
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61547 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 7QSK

7qsk


Accession code: 7QSK / Source name: PDB / Type: experimental model

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