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- EMDB-3731: Mitochondrial complex I in the deactive state -

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Basic information

Entry
Database: EMDB / ID: EMD-3731
TitleMitochondrial complex I in the deactive stateRespiratory complex I
Map data
SampleMitochondrial complex I in the deactive stateRespiratory complex I
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • Acyl carrier protein, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • (ligand) x 5
Function / homology
Function and homology information


RHOG GTPase cycle / Complex I biogenesis / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Respiratory electron transport / cardiac muscle tissue development / gliogenesis / neural precursor cell proliferation / NADH dehydrogenase activity / mitochondrial respirasome ...RHOG GTPase cycle / Complex I biogenesis / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Respiratory electron transport / cardiac muscle tissue development / gliogenesis / neural precursor cell proliferation / NADH dehydrogenase activity / mitochondrial respirasome / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / Neutrophil degranulation / oxygen sensor activity / mitochondrial ribosome / mitochondrial respiratory chain complex I / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / acyl binding / cellular response to interferon-beta / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / mitochondrial translation / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / neurogenesis / quinone binding / apoptotic mitochondrial changes / reactive oxygen species metabolic process / ATP metabolic process / aerobic respiration / cellular response to retinoic acid / respirasome / extrinsic apoptotic signaling pathway / respiratory electron transport chain / fatty acid binding / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / mitochondrial membrane / regulation of mitochondrial membrane potential / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / apoptotic signaling pathway / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / nervous system development / brain development / mitochondrial inner membrane / response to oxidative stress / structural constituent of ribosome / mitochondrial matrix / oxidoreductase activity / negative regulation of transcription, DNA-templated / protein-containing complex binding / mitochondrion / integral component of membrane / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Zinc-finger domain / Zinc finger, CHCC-type / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-quinone oxidoreductase, chain I / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase subunit D/H / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-quinone oxidoreductase, subunit D / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH:ubiquinone oxidoreductase, subunit G / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH dehydrogenase, subunit C / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase / SLBB domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase subunit E-like / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Similarity search - Component
Biological speciesBos taurus (cattle) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.13 Å
AuthorsBlaza JN / Vinothkumar KR / Hirst J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105663141 United Kingdom
Medical Research Council (United Kingdom)U105184322 United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structure of the Deactive State of Mammalian Respiratory Complex I.
Authors: James N Blaza / Kutti R Vinothkumar / Judy Hirst /
Abstract: Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner ...Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.
History
DepositionMay 23, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJan 17, 2018-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o31
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3731.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 360 pix.
= 496.8 Å
1.38 Å/pix.
x 360 pix.
= 496.8 Å
1.38 Å/pix.
x 360 pix.
= 496.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.31578538 - 1.4502776
Average (Standard dev.)0.00006563608 (±0.02169862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 496.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z496.800496.800496.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3161.4500.000

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Supplemental data

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Sample components

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Entire Mitochondrial complex I in the deactive state

EntireName: Mitochondrial complex I in the deactive stateRespiratory complex I
Number of Components: 50

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Component #1: protein, Mitochondrial complex I in the deactive state

ProteinName: Mitochondrial complex I in the deactive stateRespiratory complex I
Recombinant expression: No
MassExperimental: 1000 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #2: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.058521 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #3: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.104531 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #4: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.464807 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #5: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.236367 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #6: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.840361 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #7: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.718777 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #8: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.688773 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #9: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.219947 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #10: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.082479 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #11: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.800186 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #12: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.327922 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #13: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.13075 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #14: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.27493 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #15: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.739734 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #16: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.294037 kDa
SourceSpecies: Bos taurus (cattle)

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Component #17: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.966627 kDa
SourceSpecies: Bovine (cattle)

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Component #18: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.119541 kDa
SourceSpecies: Bovine (cattle)

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Component #19: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.203414 kDa
SourceSpecies: Bovine (cattle)

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Component #20: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.083544 kDa
SourceSpecies: Bovine (cattle)

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Component #21: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.772021 kDa
SourceSpecies: Bovine (cattle)

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Component #22: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.117445 kDa
SourceSpecies: Bovine (cattle)

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Component #23: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.860488 kDa
SourceSpecies: Bovine (cattle)

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Component #24: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.836698 kDa
SourceSpecies: Bovine (cattle)

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Component #25: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.491347 kDa
SourceSpecies: Bovine (cattle)

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Component #26: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.978148 kDa
SourceSpecies: Bovine (cattle)

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.469059 kDa
SourceSpecies: Bovine (cattle)

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Component #28: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.739855 kDa
SourceSpecies: Bovine (cattle)

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Component #29: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.443468 kDa
SourceSpecies: Bos taurus (cattle)

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.315777 kDa
SourceSpecies: Bos taurus (cattle)

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Component #31: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.230603 kDa
SourceSpecies: Bos taurus (cattle)

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Component #32: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.297649 kDa
SourceSpecies: Bovine (cattle)

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Component #33: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.906949 kDa
SourceSpecies: Bovine (cattle)

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Component #34: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.115508 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: Heart

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Component #35: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 77.044078 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ Or Tissue: heart

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Component #36: protein, NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.451367 kDa
SourceSpecies: Bovine (cattle)

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Component #37: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.361272 kDa
SourceSpecies: Bovine (cattle)

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Component #38: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.55172 kDa
SourceSpecies: Bovine (cattle)

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Component #39: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.564387 kDa
SourceSpecies: Bovine (cattle)

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Component #40: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.752357 kDa
SourceSpecies: Bovine (cattle)

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Component #41: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydr...

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.923204 kDa
SourceSpecies: Bovine (cattle)

+
Component #42: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.992936 kDa
SourceSpecies: Bovine (cattle)

+
Component #43: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.075063 kDa
SourceSpecies: Bovine (cattle)

+
Component #44: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.696693 kDa
SourceSpecies: Bovine (cattle)

+
Component #45: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.369262 kDa
SourceSpecies: Bovine (cattle)

+
Component #46: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

+
Component #47: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

+
Component #48: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

+
Component #49: ligand, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.743405 kDa

+
Component #50: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL / pH: 7.55
Support filmThe grid was PEGylated before use
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 80 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 101499.0 X (calibrated) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1300.0 - 3100.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 2954 / Sampling Size: 14 µm

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 125006 / Details: Images were normalised in Relion
3D reconstructionSoftware: RELION
CTF correction: CTF correction was done per particle after the CTF was estimated on the whole micrograph.
Resolution: 4.13 Å / Resolution Method: FSC 0.143 CUT-OFF
Euler angles: Relion uses projection matching in a ML statistical framework
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL / Overall BValue: 78.7
Output model

+
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