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- PDB-5ldw: Structure of mammalian respiratory Complex I, class1 -

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Database: PDB / ID: 5ldw
TitleStructure of mammalian respiratory Complex I, class1
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
KeywordsOXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria / oxidoreductase
Function / homologyNADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Thioredoxin-like superfamily / 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 ...NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Thioredoxin-like superfamily / 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 / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Proton-conducting membrane transporter / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / 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 / Tim17/Tim22/Tim23/Pmp24 family / 2Fe-2S ferredoxin-like superfamily / Deoxynucleoside kinase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / 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:ubiquinone oxidoreductase, ESSS subunit / [NiFe]-hydrogenase, large subunit / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / 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 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH-quinone oxidoreductase, chain G, C-terminal / Respiratory-chain NADH dehydrogenase 20 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 subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Carrier protein (CP) domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 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 / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Phosphopantetheine attachment site. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH 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, NDUFB6/B17 subunit / NADH-ubiquinone oxidoreductase MWFE subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / 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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain
Function and homology information
Specimen sourceBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.27 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
Abstract: Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive ...Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 28, 2016 / Release: Sep 7, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 7, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Derived calculations / Refinement descriptionem_3d_fitting / em_software / pdbx_struct_conn_angle_em_3d_fitting.target_criteria / _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
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, NDUFA10,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, NDUFS6,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, NDUFA8
Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13
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, NDUFA3
c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2
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, NDUFB5
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, NDUFB6
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, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,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, NDUFB9
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,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,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)891,58256
Polyers887,85645
Non-polymers3,72711
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)185390
ΔGint (kcal/M)-1604
Surface area (Å2)328110
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 / Details: Residues 28-50 are disordered or poor density / Source: (natural) Bos taurus (cattle)
References: UniProt:P03898, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#8: Protein/peptide NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35688.773 Da / Num. of mol.: 1 / Details: Residues 201-217 are disordered / Source: (natural) Bos taurus (cattle)
References: UniProt:P03887, EC:1.6.5.3 (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, EC:1.6.5.3 (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, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#12: Protein/peptide NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68327.922 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt:P03920, EC:1.6.5.3 (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, EC:1.6.5.3 (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, EC:1.6.5.3 (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 an iron-sulphur cluster (SF4)
Source: (natural) Bos taurus (cattle)
References: UniProt:P42026, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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: Residues 51-60 not modelled 129 is R for Cambridge cows instead of Q
Source: (natural) Bos taurus (cattle)
References: UniProt:P17694, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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 2 iron-sulphur clusters (SF4)
Source: (natural) Bos taurus (cattle)
References: UniProt:P42028, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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, NDUFS6,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 atom / 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: 12563.475 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 an iron-sulphur cluster (FES)
Source: (natural) Bos taurus (cattle)
References: UniProt:P04394, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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 SF4 and also binds FMN / Source: (natural) Bos taurus (cattle)
References: UniProt:P25708, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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 / Complex I-75kD / CI-75kD


Mass: 71847.797 Da / Num. of mol.: 1
Details: This chain coordinates 2xSF4 and 1FES. We are uncertain of the register 210-692
Source: (natural) Bos taurus (cattle)
References: UniProt:P15690, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone)), EC:1.6.99.3 (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, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


Mass: 34256.562 Da / Num. of mol.: 1 / Details: We are uncertain of the register 5-90 / Source: (natural) Bos taurus (cattle) / References: UniProt:P34942
#16: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9


Mass: 25549.350 Da / Num. of mol.: 1
Details: Residue range 187-199, 253-279 not modelled and none of the residues are assigned as the density ...Residue range 187-199, 253-279 not modelled and none of the residues are assigned as the density doesn't allow it. The density for NAP is prominent and has been modelled.
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: 15083.544 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, NDUFA8 / 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
#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: 14772.021 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt:Q8HXG6
#25: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13, NDUFA13 / 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, NDUFA3 / 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: 17115.508 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, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUFC2 / 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, NDUFB5 / 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, NDUFB6 / 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, NDUFB4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, NDUFB4,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, NDUFB9 / 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: 16297.649 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt:Q02368
#41: 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,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,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

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


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4
#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 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
Source: NATURAL
Molecular weightValue: 1 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Cellular location: Mitochondria / Organ: Heart / Organelle: Mitochondria / Organism: Bos taurus (cattle)
Buffer solutionDetails: 20 mM TRIS-HCL, 150 mM NaCl, 0.03% CYMAL-7 / pH: 8
Buffer componentConc.: 150 mg/ml / Units: 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 discharge 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 present in a cold room, 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 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 87.5 kelvins / Temperature (min): 87.5 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/A2
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 fittingManual model building, corrections were done with Coot
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 correction wad done per particle after the 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: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 48033 / Nominal pixel size: 1.33 / Actual pixel size: 1.33 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 83.049 / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: Maximum likelihood
Least-squares processHighest resolution: 4.27 Å
Number of atoms included #1Total: 51117
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01952020
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.2692.05271480
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.9655.0007737
ELECTRON MICROSCOPYr_dihedral_angle_2_deg39.00422.7791310
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.51415.0005744
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.86015.000201
ELECTRON MICROSCOPYr_chiral_restr0.0890.2008780
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02139420
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_it0.6949.60131110
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it1.30814.39738793
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it0.3398.89720910
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined6.26678.79174815
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 4.27 Å / R factor R work: 0.526 / Lowest resolution: 4.381 Å / Number reflection R free: 0 / Number reflection R work: 218869 / Total number of bins used: 20 / Percent reflection obs: 1

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