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- PDB-6g72: Mouse mitochondrial complex I in the deactive state -

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Entry
Database: PDB / ID: 6g72
TitleMouse mitochondrial complex I in the deactive state
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
KeywordsOXIDOREDUCTASE / Complex I / mitochondria / proton pump / membrane protein / oxidoreductase
Function / homologyTim17/Tim22/Tim23/Pmp24 family / 2Fe-2S ferredoxin-like superfamily / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 ...Tim17/Tim22/Tim23/Pmp24 family / 2Fe-2S ferredoxin-like superfamily / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Deoxynucleoside kinase domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Thioredoxin-like superfamily / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Proton-conducting membrane transporter / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH dehydrogenase / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NAD(P)-binding domain superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase, subunit 10 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 5, C-terminal / NmrA-like domain / NADH:ubiquinone oxidoreductase, B18 subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase, subunit b14.5b / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, MNLL subunit / Molybdopterin oxidoreductase / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 4Fe-4S dicluster domain / Glyoxylate metabolism and glycine degradation / 2Fe-2S iron-sulfur cluster binding domain / Thioredoxin-like [2Fe-2S] ferredoxin / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Neutrophil degranulation / Respiratory electron transport / Mitochondrial protein import / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsAgip, A.N.A. / Blaza, J.N. / Bridges, H.R. / Viscomi, C. / Rawson, S. / Muench, S.P. / Hirst, J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states.
Authors: Ahmed-Noor A Agip / James N Blaza / Hannah R Bridges / Carlo Viscomi / Shaun Rawson / Stephen P Muench / Judy Hirst
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 4, 2018 / Release: Jun 6, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 6, 2018Structure modelrepositoryInitial release
1.1Jul 4, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Aug 1, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.3Oct 3, 2018Structure modelData collection / Experimental preparationem_sample_support_em_sample_support.grid_type

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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)1,052,14559
Polyers1,046,82045
Non-polymers5,32514
Water0
1


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/peptide NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


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


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


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


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


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


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


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

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

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


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


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


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


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


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


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


Mass: 12675.772 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q99LY9

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

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


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


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


Mass: 11833.504 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q8BK30

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Protein/peptide , 2 types, 3 molecules GTU

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


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


Mass: 17390.289 Da / Num. of mol.: 2 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CR21

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

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


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


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


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


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


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


Mass: 20025.127 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9DCJ5
#24: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 15130.416 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: G5E814
#25: Protein/peptide 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 and interferon-induced mortality 19 protein / Gene associated with retinoic and IFN-induced mortality 19 protein / NADH-ubiquinone oxidoreductase B16.6 subunit


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


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


Mass: 9380.904 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQ91
#42: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


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


Mass: 12637.629 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9Z1P6

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

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


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


Mass: 14185.692 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9CQ54

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

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


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


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


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


Mass: 15582.122 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q3UIU2
#35: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / CI-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


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


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


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


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


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


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


Mass: 21054.832 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: Q9DCS9

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Non-polymers , 7 types, 14 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4 / Iron–sulfur cluster
#46: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#47: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / Flavin mononucleotide
#48: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#49: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#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 / Formula: C25H49N2O9PS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial complex I from mouse in the deactive state
Type: COMPLEX
Details: Placed in the deactive state by heating to 37degC for 30 mins before isolation
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44
Source: NATURAL
Molecular weightValue: 1.0 MDa / Experimental value: NO
Source (natural)Organ: Heart / Organism: Mus musculus (house mouse) / Strain: C57BL/6
Buffer solutionpH: 7.14
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMSodium chlorideNaCl1
220 mMTris1
30.05 %DDM1
SpecimenConc.: 3 mg/ml
Details: Peak fraction from a gel filtration column- monodisperse and not concentrated. The complex was put into the deactive state by heating at 37degC for 30 mins before isolation in detergent.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gold was PEGylated prior to use in anaerobic ethanol in 5mM SPT-11P6 (Sensopath Technologies) for two days 0.6/1 holes
Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: 8-16s blotting.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37600 / Nominal defocus max: 3400 nm / Nominal defocus min: 2200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 30 / Used frames/image: 1-30

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPU1.9image acquisition
4Gctf1.06CTF correction
7Coot0.8.9.1model fitting
9RELION2.1initial Euler assignmentpatch b1
10RELION2.1final Euler assignmentpatch b1
11RELION2.1classificationpatch b1
12RELION2.13D reconstructionpatch b1
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Manually picked / Number of particles selected: 40131
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17066 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: Used default paramteres in phenix.real_space_refine
Ref protocol: FLEXIBLE FIT / Ref space: REAL

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