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- PDB-9ti4: High resolution Cryo-EM structure of human complex I in mitochondria -

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Basic information

Entry
Database: PDB / ID: 9ti4
TitleHigh resolution Cryo-EM structure of human complex I in mitochondria
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 / Human mitochondria / respirasome complex / complex I / NADH dehydrogenase
Function / homology
Function and homology information


mitochondrial large ribosomal subunit assembly / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex I biogenesis / Respiratory electron transport / protein insertion into mitochondrial inner membrane / protein lipoylation / ubiquinone biosynthetic process / blastocyst hatching / Mitochondrial ribosome-associated quality control ...mitochondrial large ribosomal subunit assembly / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex I biogenesis / Respiratory electron transport / protein insertion into mitochondrial inner membrane / protein lipoylation / ubiquinone biosynthetic process / blastocyst hatching / Mitochondrial ribosome-associated quality control / cellular respiration / response to light intensity / Mitochondrial translation termination / cellular response to oxygen levels / Mitochondrial protein import / mesenchymal stem cell proliferation / iron-sulfur cluster assembly complex / reproductive system development / mitochondrial large ribosomal subunit binding / respiratory chain complex / gliogenesis / mitochondrial [2Fe-2S] assembly complex / mesenchymal stem cell differentiation / circulatory system development / negative regulation of non-canonical NF-kappaB signal transduction / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / positive regulation of mitochondrial membrane potential / response to hydroperoxide / cardiac muscle tissue development / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / cellular response to glucocorticoid stimulus / oxidoreductase activity, acting on NAD(P)H / azurophil granule membrane / stem cell division / iron-sulfur cluster assembly / sodium ion transport / ubiquinone binding / acyl binding / electron transport coupled proton transport / regulation of protein phosphorylation / NADH:ubiquinone reductase (H+-translocating) / acyl carrier activity / mitochondrial ATP synthesis coupled electron transport / positive regulation of ATP biosynthetic process / NADH dehydrogenase activity / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / RHOG GTPase cycle / respiratory chain complex I / positive regulation of execution phase of apoptosis / response to cAMP / NADH dehydrogenase (ubiquinone) activity / endopeptidase activator activity / quinone binding / cellular response to interferon-beta / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / neurogenesis / ionotropic glutamate receptor binding / substantia nigra development / Mitochondrial protein degradation / reactive oxygen species metabolic process / muscle contraction / cerebellum development / fatty acid binding / aerobic respiration / synaptic membrane / regulation of mitochondrial membrane potential / respiratory electron transport chain / response to nicotine / DNA damage response, signal transduction by p53 class mediator / kidney development / response to hydrogen peroxide / monooxygenase activity / sensory perception of sound / circadian rhythm / fatty acid metabolic process / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / multicellular organism growth / NAD binding / fatty acid biosynthetic process / positive regulation of protein catabolic process / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / protease binding / gene expression / response to ethanol / in utero embryonic development / response to hypoxia / electron transfer activity
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 / NADH-ubiquinone oxidoreductase, subunit 10 ...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 / 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 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / 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 oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2.
Similarity search - Domain/homology
Chem-8Q1 / CARDIOLIPIN / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial ...Chem-8Q1 / CARDIOLIPIN / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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 7 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsNguyen, M.D. / Singh, V. / Rorbach, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome.
Authors: Minh Duc Nguyen / Ana Sierra-Magro / Vivek Singh / Anas Khawaja / Alba Timón-Gómez / Antoni Barrientos / Joanna Rorbach /
Abstract: The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required ...The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required for ATP synthesis. These complexes can associate into supercomplexes (SCs), such as the CI + CIII₂ + CIV respirasome, but how SCs form, by joining preassembled complexes or by engaging partially assembled intermediates, remains unresolved. Here, we use cryo-electron microscopy to determine high-resolution structures of native human CI + CIII₂ + CIV late-assembly intermediates. Together with biochemical analyses, these structures show that respirasome biogenesis concludes with the final maturation of CIV while it is associated with fully assembled CI and CIII₂. We identify HIGD2A as a placeholder factor within isolated and supercomplexed CIV that is replaced by subunit NDUFA4 during the last step of CIV and respirasome assembly. This mechanism suggests that placeholders such as HIGD2A act as molecular timers, preventing premature incorporation of NDUFA4 or its isoforms and ensuring the orderly progression of pre-SC particles into functional respirasomes. Since defects in CIV assembly, including NDUFA4 deficiencies, cause severe encephalomyopathies and neurodegenerative disorders, understanding the molecular architecture and assembly pathways of isolated and supercomplexed CIV offers insight into the pathogenic mechanisms underlying these conditions.
History
DepositionDec 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 25, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)969,15580
Polymers944,45145
Non-polymers24,70435
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NDUFV1 / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone ...NDUFV1 / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 47680.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P49821, NADH:ubiquinone reductase (H+-translocating)
#9: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / CI-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit / Renal carcinoma antigen NY-REN-4


Mass: 4623.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56181
#13: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NDUFV2 / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 23430.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P19404, NADH:ubiquinone reductase (H+-translocating)

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

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit / TYKY subunit


Mass: 20314.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O00217, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit / PSST subunit


Mass: 18449.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O75251, NADH:ubiquinone reductase (H+-translocating)
#10: 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: 14064.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43181
#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 24432.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O75489, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 49249.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O75306, NADH:ubiquinone reductase (H+-translocating)
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 10716.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75380
#30: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12445.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43920

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

#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / LYR motif-containing protein 6 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 14205.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56556
#5: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 9722.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43678
#7: 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: 13119.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16718
#8: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 38848.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16795
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / 13 kDa differentiation-associated protein / Complex I-B17.2 / CI-B17.2 / CIB17.2 / NADH-ubiquinone ...13 kDa differentiation-associated protein / Complex I-B17.2 / CI-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 17011.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UI09
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8084.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15239
#18: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9156.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95167
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14736.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86Y39
#20: 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 / GRIM-19 / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 16360.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J0
#41: 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: 20007.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51970
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 37200.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95299
#44: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Complex I-B14.5a / CI-B14.5a / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12571.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95182

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Protein , 2 types, 3 molecules HXM

#6: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9976.442 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561
#11: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Complex I-75kD / CI-75kD


Mass: 75471.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28331, NADH:ubiquinone reductase (H+-translocating)

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

#21: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 7624.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95178
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / CI-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 9575.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43676
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 16573.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43674
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 14491.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95139
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / CI-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18094.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95169
#26: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 20489.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O96000
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit / Neuronal protein 17.3 / ...Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit / Neuronal protein 17.3 / Np17.3 / p17.3


Mass: 12590.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX14
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / CI-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6514.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75438
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 15100.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95168
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / LYR motif-containing protein 3 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21246.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6M9
#42: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cell adhesion protein SQM1 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 14854.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17568

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

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


Mass: 5904.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43677
#29: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / Human lung cancer oncogene 1 protein / HLC-1 / NADH-ubiquinone ...Complex I-B14.5b / CI-B14.5b / Human lung cancer oncogene 1 protein / HLC-1 / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 14209.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95298

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

#31: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 38980.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03891, NADH:ubiquinone reductase (H+-translocating)
#32: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13189.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03897, NADH:ubiquinone reductase (H+-translocating)
#33: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L / ND4L


Mass: 10745.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03901, NADH:ubiquinone reductase (H+-translocating)
#34: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 66836.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03915, NADH:ubiquinone reductase (H+-translocating)
#35: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18512.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03923, NADH:ubiquinone reductase (H+-translocating)
#39: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51613.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03905, NADH:ubiquinone reductase (H+-translocating)
#40: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35447.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P03886, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 12 types, 36 molecules

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


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#47: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#48: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#51: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM
#52: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 6 / 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 / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#56: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

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Sample preparation

ComponentName: NADH-ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Details: 25 mM HEPES-KOH pH=7.5, 50 mM KCl, 20 mM Mg(OAc)2, 0.01% (v/v) Lauryl Maltose Neopentyl Glycol (LMNG), 0.001 % cardiolipin, 0.001 % glycol-diosgenin (GDN, Sigma-Aldrich), 0.1mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
4cryoSPARCCTF correction
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2508182
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236346 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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