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- PDB-9ihq: Closed state with NUQM and without flavoprotein (classification s... -

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Entry
Database: PDB / ID: 9ihq
TitleClosed state with NUQM and without flavoprotein (classification state 2) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs
Components
  • (Acyl carrier ...) x 2
  • (NADH dehydrogenase [ubiquinone] ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • Altered inheritance of mitochondria protein 41, mitochondrial
  • BA75_00589T0
  • BA75_00622T0
  • BA75_04796T0
  • BA75_05084T0
  • NADH-ubiquinone oxidoreductase
  • NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
  • Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM
  • Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
KeywordsMEMBRANE PROTEIN / NADH:ubiquinone oxidoreductase nanodisc membrane protein complex
Function / homology
Function and homology information


carbon-nitrogen ligase activity, with glutamine as amido-N-donor / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) ...carbon-nitrogen ligase activity, with glutamine as amido-N-donor / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / acyl binding / ubiquinone 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 / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / NAD 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
Uncharacterised protein YqeY/Aim41 / YqeY/Aim41, N-terminal domain / Yqey-like protein / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / 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 / : ...Uncharacterised protein YqeY/Aim41 / YqeY/Aim41, N-terminal domain / Yqey-like protein / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / 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 dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / : / 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-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH 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 / 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 / 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-quinone oxidoreductase, chain M/4 / 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 / 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-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 / 2Fe-2S iron-sulfur cluster binding domain / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / : / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / Altered inheritance of mitochondria protein 41, mitochondrial ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / : / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / Altered inheritance of mitochondria protein 41, mitochondrial / Uncharacterized protein / NADH-ubiquinone oxidoreductase 78 kDa subunit, mitochondrial / NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / BA75_00622T0 / NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NADH-ubiquinone oxidoreductase / NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / BA75_00589T0 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / BA75_05084T0 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / BA75_04796T0 / NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / Acyl carrier protein / Acyl carrier protein / NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I) / NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
Similarity search - Component
Biological speciesKomagataella pastoris (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGrba, D.N. / Hirst, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: Global conformations of complex I are distinguished by the binding of a unique interdomain bridging subunit.
Authors: Chris Seunggyu Lee / Daniel N Grba / John J Wright / Bozhidar S Ivanov / Judy Hirst /
Abstract: Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. ...Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. During ischemia, mammalian CI transitions from a turnover-ready, structurally "closed" state toward a dormant "open" state that prevents it from functioning in reverse during reperfusion to produce reactive oxygen species. Unfortunately, simpler, genetically tractable CI models do not recapitulate the same regulatory behavior, compromising mechanistic studies. Here, we report the structure of isolated CI from the yeast (-CI) and identify distinct closed and open states that resemble those of mammalian CI. Notably, a hitherto-unknown protein (NUQM) completes an interdomain bridge in only the closed state, implying that NUQM stabilizes it by restricting the conformational changes of opening. The direct correlation of NUQM binding with closed/open status in -CI provides opportunities for investigating regulatory mechanisms relevant to reversible catalysis and ischemia-reperfusion injury.
History
DepositionFeb 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
1: Altered inheritance of mitochondria protein 41, mitochondrial
A: NADH-ubiquinone oxidoreductase chain 3
B: BA75_00622T0
C: NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
D: NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
G: NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
H: NADH-ubiquinone oxidoreductase chain 1
I: NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
J: NADH-ubiquinone oxidoreductase chain 6
K: NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
O: NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
P: NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
R: NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
S: NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
T: Acyl carrier protein
U: Acyl carrier protein
V: NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
W: BA75_04796T0
X: NADH-ubiquinone oxidoreductase
Y: NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
c: BA75_00589T0
d: Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM
e: BA75_05084T0
f: NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
g: NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
h: NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
i: NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
j: Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
k: NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
l: NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
m: NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,006,803100
Polymers966,74042
Non-polymers40,06258
Water00
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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Protein , 28 types, 28 molecules 1BCDGIKOPRSVWXYbcdefghijklmp

#1: Protein Altered inheritance of mitochondria protein 41, mitochondrial / NUQM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 22019.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: C4QXX8
#3: Protein BA75_00622T0 / NUKM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 23353.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB5, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NUGM (30 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 33183.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB1, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NUCM (49 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 54962.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWA8, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NUAM (75 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 79646.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWA6, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NUIM (TYKY) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 25544.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB3, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NULM (ND4L) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 9118.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB6, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NUXM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 22263.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB9, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NUEM (39 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 43349.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWA9, NADH:ubiquinone reductase (H+-translocating)
#17: Protein NUMM (13 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 15717.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB7, NADH:ubiquinone reductase (H+-translocating)
#18: Protein NI8M (B8) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 9858.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD3, NADH:ubiquinone reductase (H+-translocating)
#21: Protein NUFM (B13) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 15590.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB0, NADH:ubiquinone reductase (H+-translocating)
#22: Protein BA75_04796T0 / NB4M (B14) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 14783.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD6, NADH:ubiquinone reductase (H+-translocating)
#23: Protein NADH-ubiquinone oxidoreductase


Mass: 20718.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWB8
#24: Protein NUJM (B14.7) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 23507.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWB4, NADH:ubiquinone reductase (H+-translocating)
#27: Protein NI9M (B9) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 9181.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD4, NADH:ubiquinone reductase (H+-translocating)
#28: Protein BA75_00589T0 / NUZM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 20110.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC1, NADH:ubiquinone reductase (H+-translocating)
#29: Protein Pichia pastoris NADH-ubiquinone oxidoreductase subunit NEBM


Mass: 9050.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: C4R4T8
#30: Protein BA75_05084T0 / NIPM (15 kDa) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 12251.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD1, NADH:ubiquinone reductase (H+-translocating)
#31: Protein NUTM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 9864.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWE5, NADH:ubiquinone reductase (H+-translocating)
#32: Protein NESM (ESSS) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 27250.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWE1, NADH:ubiquinone reductase (H+-translocating)
#33: Protein NUSM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 21224.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWE4, NADH:ubiquinone reductase (H+-translocating)
#34: Protein NUUM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 8335.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWE6, NADH:ubiquinone reductase (H+-translocating)
#35: Protein Subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 7071.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: A0A1G4KQ11
#36: Protein NB2M (B12) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 7141.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD5, NADH:ubiquinone reductase (H+-translocating)
#37: Protein NIAM (ASHI) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 17944.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC8, NADH:ubiquinone reductase (H+-translocating)
#38: Protein NB5M (B15) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 9437.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWD7, NADH:ubiquinone reductase (H+-translocating)
#41: Protein NIDM (PDSW) subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 10787.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC9, NADH:ubiquinone reductase (H+-translocating)

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NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJLMN

#2: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 16019.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC4, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 39698.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC2, NADH:ubiquinone reductase (H+-translocating)
#9: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 18564.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC7, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 72436.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC6, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 54784.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC5, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 59097.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus)
References: UniProt: E1UWC3, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] ... , 6 types, 6 molecules QZanoq

#16: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 18241.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWC0
#25: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 17243.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWD8
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 17446.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWD0
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 12845.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWD2
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 10473.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWD9
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit


Mass: 16331.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWE0

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Acyl carrier ... , 2 types, 2 molecules TU

#19: Protein Acyl carrier protein


Mass: 15507.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWE2
#20: Protein Acyl carrier protein / NEBM subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I)


Mass: 14780.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella pastoris (fungus) / References: UniProt: E1UWE3

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Non-polymers , 9 types, 58 molecules

#43: Chemical...
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#44: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#45: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#46: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#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.: 21 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#48: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#49: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#51: 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 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: Pichia Pastoris (Komagataella phaffi) mitochondrial complex I (NADH:ubiquinone oxidoreductase)
Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 0.850 MDa / Experimental value: YES
Source (natural)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.5
Details: 10 mM MOPS, 50 mM KCl, pH 7.5 at 4 degrees celsius.
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMMOPS1
250 mMpotassium chlorideKCl1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: LMNG-solubilised Pichia Pastoris CI reconstituted in to nanodiscs (8:1:1 ratio of DOPC:DOPE:CDL [0.5 mg total] and 20 nM final Q10)
Specimen supportDetails: glow discharged for 2X 90s, flipping the grid in between
Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 2s blot time and -10 blot force

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.85 sec. / Electron dose: 47.79 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7574
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1350752
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61256 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: The initial model was made for state 1 and then subunits removed to match this state. This was manually inspected in Coot and final refinements with ligand restraints imposed performed in PHENIX v.1.21_5207
Atomic model buildingPDB-ID: 9IHR

9ihr


Accession code: 9IHR / Details: State 1 from same data / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 37.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003165509
ELECTRON MICROSCOPYf_angle_d0.466288572
ELECTRON MICROSCOPYf_chiral_restr0.04039725
ELECTRON MICROSCOPYf_plane_restr0.003711010
ELECTRON MICROSCOPYf_dihedral_angle_d13.162424676

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