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- PDB-5lc5: Structure of mammalian respiratory Complex I, class2 -

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Database: PDB / ID: 5lc5
TitleStructure of mammalian respiratory Complex I, class2
Components
  • (Acyl carrier protein, ...) x 2
  • (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
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1
KeywordsOXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria / Oxidoreductase
Function / homologyTim17/Tim22/Tim23/Pmp24 family / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase ...Tim17/Tim22/Tim23/Pmp24 family / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Proton-conducting membrane transporter / ACP-like superfamily / Molybdopterin oxidoreductase / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Phosphopantetheine attachment site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Deoxynucleoside kinase / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / Thioredoxin-like superfamily / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / Zinc finger, CHCC-type / 2Fe-2S ferredoxin-like superfamily / 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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Deoxynucleoside kinase domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / Carrier protein (CP) domain profile. / 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 subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Respiratory electron transport / Neutrophil degranulation / Complex I biogenesis / Thioredoxin-like [2Fe-2S] ferredoxin / 2Fe-2S iron-sulfur cluster binding domain / 4Fe-4S dicluster domain / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / GRIM-19 protein / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH dehydrogenase subunit 2 C-terminus / NADH dehydrogenase subunit 5 C-terminus / CHCH domain / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / MNLL subunit / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Phosphopantetheine attachment site. / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-ubiquinone oxidoreductase subunit 10 / Zinc-finger domain / SLBB domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 4Fe-4S dicluster domain / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.35 Å resolution
AuthorsVinothkumar, K.R. / Zhu, J. / Hirst, J.
Funding supportUnited Kingdom , 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105184322/U105663141United Kingdom
CitationJournal: Nature / Year: 2016
Title: Structure of mammalian respiratory complex I.
Authors: Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2016 / Release: Sep 7, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 7, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.name / _em_software.version
1.2Aug 23, 2017Structure modelSource and taxonomy / Structure summaryentity / entity_src_gen / entity_src_nat_entity.src_method

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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,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1
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, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,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,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,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,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,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,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,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,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,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,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8
m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,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, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7
s: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)885,28556
Polyers881,55845
Non-polymers3,72711
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)189940
ΔGint (kcal/M)-1625
Surface area (Å2)326800
MethodPISA

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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: 12510.898 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03898, NADH:ubiquinone reductase (H+-translocating)
#8: Protein/peptide NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35084.062 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03887, NADH:ubiquinone reductase (H+-translocating)
#10: Protein/peptide NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18622.936 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03924, NADH:ubiquinone reductase (H+-translocating)
#11: Protein/peptide NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10437.718 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03902, NADH:ubiquinone reductase (H+-translocating)
#12: Protein/peptide NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68067.609 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03920, NADH:ubiquinone reductase (H+-translocating)
#13: Protein/peptide NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51886.402 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03910, NADH:ubiquinone reductase (H+-translocating)
#14: Protein/peptide NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 38901.461 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03892, NADH:ubiquinone reductase (H+-translocating)

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

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


Mass: 16625.518 Da / Num. of mol.: 1 / Details: This chain coordinates Iron-sulphur cluster. / Source: (natural) Bos taurus (cattle)
References: UniProt: P42026, 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: 24202.396 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P23709, 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: 48693.758 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P17694, 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 / TYKY subunit


Mass: 20219.947 Da / Num. of mol.: 1 / Details: This chain coordinates two SF4. / Source: (natural) Bos taurus (cattle)
References: UniProt: P42028, 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: 9634.868 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#18: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 8316.853 Da / Num. of mol.: 1 / Details: This chain coordinates a Zinc ion. / Source: (natural) Bos taurus (cattle) / References: UniProt: P23934
#31: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


Mass: 12694.671 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02379

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

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


Mass: 27341.496 Da / Num. of mol.: 1 / Details: This chain coordinates one FES. / Source: (natural) Bos taurus (cattle)
References: UniProt: P04394, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#6: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


Mass: 50718.777 Da / Num. of mol.: 1
Details: This chain coordinates two iron-sulfur clusters and also binds Flavin mono nucleotide.
Source: (natural) Bos taurus (cattle)
References: UniProt: P25708, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#45: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3


Mass: 2996.685 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)

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Protein/peptide , 1 types, 1 molecules G

#7: Protein/peptide NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1 / Complex I-75kD / CI-75kD


Mass: 66442.281 Da / Num. of mol.: 1
Details: This chain coordinates one binuclear FES and two SF4.
Source: (natural) Bos taurus (cattle)
References: UniProt: P15690, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

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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, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 34014.227 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P34942
#16: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 28528.021 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#19: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


Mass: 9270.575 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02370
#22: 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: 13334.608 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P23935
#23: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 15083.544 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02366
#24: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,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: 18115.223 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P42029
#25: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14412.514 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG6
#26: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,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-interferon-induced mortality 19 protein / GRIM-19 / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 14135.900 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q95KV7
#27: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8117.445 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02377
#28: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 7860.488 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02371
#43: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


Mass: 16309.545 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: O97725
#44: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7


Mass: 7422.140 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)

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

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


Mass: 8672.939 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P52505
#21: Protein/peptide Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9846.298 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P52505

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

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


Mass: 8796.211 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02376
#30: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / NADH-ubiquinone oxidoreductase subunit B14.5b


Mass: 11988.300 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02827

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

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


Mass: 6978.148 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02378
#33: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 17594.945 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG5
#34: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 18069.865 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02380
#35: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 11636.995 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02367
#36: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2


Mass: 4443.468 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#37: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3


Mass: 6315.777 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#38: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8


Mass: 10060.393 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#39: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


Mass: 13415.493 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P48305
#40: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 19246.094 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02369
#41: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 7583.900 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02368
#42: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


Mass: 16906.949 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02373

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Non-polymers , 5 types, 11 molecules

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


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


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


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / Flavin mononucleotide
#49: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Formula: C21H28N7O17P3 / Nicotinamide adenine dinucleotide phosphate
#50: Chemical ChemComp-ZN / ZINC ION


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

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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: Bovine respiratory Complex I / Type: COMPLEX
Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
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, 45
Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Cellular location: Mitochondria / Organ: Heart / Organelle: Mitochondria / Organism: Bos taurus (cattle)
Buffer solutionpH: 8
Buffer componentConc.: 150 mM / Name: sodium chloride / Formula: NaCl
SpecimenConc.: 3.5 mg/ml
Details: Enzyme was purified from bovine heart mitochondria. The detergent used for the final step is cymal-7.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins
Details: The specimen was vitrified in an environmental plunge-freeze apparatus, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged.

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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 / Nominal magnification: 59000 / Calibrated magnification: 105263 / Calibrated defocus min: 1800 nm / Calibrated defocus max: 5500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 85 kelvins / Temperature (min): 85 kelvins
Image recordingAverage exposure time: 2 sec. / Electron dose: 35 e/Å2
Details: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2s
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096 / Movie frames/image: 34 / Used frames/image: 1-34

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Processing

SoftwareName: REFMAC / Version: 5.8.0134 / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4CTF correctionCTF was estimated on the full image
7Coot0.8.3model fittingCoot was used for manual model building and fixing geometry related issues
9REFMAC5.8.0134model refinement
11RELION1.4final Euler assignmentMaximum Likelihood
12RELION1.4classificationMaximum Likelihood
13RELION1.43D reconstructionMaximum Likelihood
Image processingDetails: Each image was exposed for 2 seconds resulting in a total dose of ~35 e/A2s. The frames were captures with a in-house protocol at 17 frames/second.
CTF correctionDetails: Ctf was estimated from the whole micrograph. Ctf was corrected per particle.
Type: NONE
Particle selectionDetails: All particles were picked manually / Number of particles selected: 139456
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 33301 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 86.75 / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: Maximum likelihood
RefineCorrelation coeff Fo to Fc: 0.945 / Overall SU B: 23.477 / Overall SU ML: 0.274 / Overall ESU R: 0.224
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 86.75 Å2 / Aniso B11: -0.3 Å2 / Aniso B12: -0.15 Å2 / Aniso B13: -0.2 Å2 / Aniso B22: -0.17 Å2 / Aniso B23: -0.3 Å2 / Aniso B33: 0.47 Å2
Least-squares processR factor R work: 0.36429 / R factor obs: 0.36429 / Highest resolution: 4.35 Å / Lowest resolution: 478.8 Å / Number reflection obs: 2793924 / Percent reflection obs: 1
Number of atoms included #1Total: 51652
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01952567
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.2812.05372251
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.0445.0007844
ELECTRON MICROSCOPYr_dihedral_angle_2_deg38.45022.7781314
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.65315.0005751
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.19615.000201
ELECTRON MICROSCOPYr_chiral_restr0.0900.2008877
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02139887
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.6609.83631523
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it1.23014.75439318
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it0.4469.64421044
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined4.12383.56275712
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 4.35 Å / R factor R work: 0.518 / Lowest resolution: 4.463 Å / Number reflection R free: 0 / Number reflection R work: 206837 / Total number of bins used: 20 / Percent reflection obs: 1

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