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- PDB-5ldx: Structure of mammalian respiratory Complex I, class3. -

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Database: PDB / ID: 5ldx
TitleStructure of mammalian respiratory Complex I, class3.
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,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsOXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria / oxidoreductase
Function / homologyTim17/Tim22/Tim23/Pmp24 family / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / 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 dehydrogenase ...Tim17/Tim22/Tim23/Pmp24 family / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / 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 dehydrogenase / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Proton-conducting membrane transporter / 2Fe-2S ferredoxin-like superfamily / Molybdopterin oxidoreductase / 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 / ETC complex I subunit conserved region / Thioredoxin-like superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / 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, iron-sulphur subunit 5 / Deoxynucleoside kinase domain / NADH-ubiquinone oxidoreductase, subunit 10 / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Complex 1 protein (LYR family) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / 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 / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / 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] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site
Function and homology information
Specimen sourceBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.6 Å resolution
AuthorsVinothkumar, K.R. / Zhu, J. / Hirst, J.
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 28, 2016 / Release: Sep 14, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 14, 2016Structure modelrepositoryInitial release
1.1Sep 28, 2016Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collectionem_software_em_software.name / _em_software.version

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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, 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,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, NDUFA9
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4
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
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
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
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
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
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
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,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, NDUFA7
s: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)872,51156
Polyers868,78445
Non-polymers3,72711
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)186080
ΔGint (kcal/M)-1612
Surface area (Å2)327270
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: 13058.521 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03898, NADH dehydrogenase (ubiquinone)
#8: Protein/peptide NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35688.773 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03887, NADH dehydrogenase (ubiquinone)
#10: Protein/peptide NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19082.479 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03924, NADH dehydrogenase (ubiquinone)
#11: Protein/peptide NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10800.186 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03902, NADH dehydrogenase (ubiquinone)
#12: Protein/peptide NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68327.922 Da / Num. of mol.: 1
Details: Note: The density for transverse helix and the last TM helix around 548-605 is poor but has been ...Note: The density for transverse helix and the last TM helix around 548-605 is poor but has been left as observed for class 1 for comparison.
Source: (natural) Bos taurus (cattle)
References: UniProt: P03920, NADH dehydrogenase (ubiquinone)
#13: Protein/peptide NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 52130.750 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03910, NADH dehydrogenase (ubiquinone)
#14: Protein/peptide NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39274.930 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P03892, NADH dehydrogenase (ubiquinone)

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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: 20104.531 Da / Num. of mol.: 1 / Details: This chain coordinates a Iron-sulphur cluster. / Source: (natural) Bos taurus (cattle)
References: UniProt: P42026, NADH dehydrogenase (ubiquinone), 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: 26464.807 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: P23709, NADH dehydrogenase (ubiquinone), 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: 49165.289 Da / Num. of mol.: 1
Details: 128 should be an R instead of Q for Cambridge cows.
Source: (natural) Bos taurus (cattle)
References: UniProt: P17694, NADH dehydrogenase (ubiquinone), 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 2x SF4 / Source: (natural) Bos taurus (cattle)
References: UniProt: P42028, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#17: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4


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 / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


Mass: 8316.853 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P23934
#30: 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: 23840.361 Da / Num. of mol.: 1 / Details: This chain coordinates FES / Source: (natural) Bos taurus (cattle)
References: UniProt: P04394, NADH dehydrogenase (ubiquinone), 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: 48562.137 Da / Num. of mol.: 1 / Details: This chain coordinates 1SF4 and binds FMN / Source: (natural) Bos taurus (cattle)
References: UniProt: P25708, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#44: 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 , 2 types, 3 molecules GTU

#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, mitochondrial / Complex I-75kD / CI-75kD


Mass: 64614.125 Da / Num. of mol.: 1 / Details: This chain coordinates 2 SF4 and 1FES / Source: (natural) Bos taurus (cattle)
References: UniProt: P15690, NADH dehydrogenase (ubiquinone), NADH dehydrogenase
#20: Protein/peptide Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 10119.541 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / References: UniProt: P52505

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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,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, NDUFA9


Mass: 24102.582 Da / Num. of mol.: 1 / Details: binds NAP / 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: 11097.824 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02370
#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: 13203.414 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P23935
#22: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 14952.349 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02366
#23: 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 / Complex I-19kD / CI-19kD / Complex I-PGIV / CI-PGIV / NADH-ubiquinone oxidoreductase 19 kDa subunit


Mass: 17617.576 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: P42029
#24: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 14640.825 Da / Num. of mol.: 1
Details: The density for this subunit is poor and the model has been taken from class1 for comparison.
Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG6
#25: 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
#26: 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
#27: 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
#42: 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
#43: 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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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: 5836.698 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02376
#29: 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

#31: 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
#32: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 14469.059 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG5
#33: 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 / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


Mass: 12614.555 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02380
#34: 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 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 10234.333 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02367
#35: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2


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


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


Mass: 10060.393 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
#38: 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 / 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
#39: 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 / 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
#40: 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
#41: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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

#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Formula: C21H28N7O17P3 / Nicotinamide adenine dinucleotide phosphate
#49: 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 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
Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Cellular location: Mitochondria / Organ: Heart / Organelle: Mitochondria / Organism: Bos taurus (cattle)
Buffer solutionName: 20 mM TRIS-HCL, 150 mM NaCl, 0.03% CYMAL-7 / pH: 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 supportDetails: holey carbon grids were placed on a filter paper in a glass petridish and pumped for around 5 minutes to remove any residual moisture. the glow of the plasma was observed and glow discharged when it was purple
Grid 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 / Nominal defocus max: 5500 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / 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: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4CTF correctionCTF was estimated on the full image
7Coot0.8.3model fitting
9PHENIX1.10_2155model 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 corrected per particle. Ctf was estimated on the whole micrograph
Type: NONE
Particle selectionDetails: All particles were picked manually / Number of particles selected: 139456
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 19306 / Nominal pixel size: 1.33 / Actual pixel size: 1.33 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: The model from Class1 (D_1200000497) was used for rigid body fitting. The B-factor for individual atoms is carried over from class 1 and doesn't mean anything.
Ref protocol: RIGID BODY FIT / Ref space: REAL

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