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- EMDB-9534: Architecture of mammalian respirasome -

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Basic information

Entry
Database: EMDB / ID: EMD-9534
TitleArchitecture of mammalian respirasome
Map data
SampleRespirasome
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • NADH-ubiquinone oxidoreductase 75 kDa subunit
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • Acyl carrier protein
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 3
  • Mitochondrial NADH dehydrogenase Fe-S protein 4
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 unknown subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (ligand) x 10
Function / homology
Function and homology information


ubiquinone-6 biosynthetic process / reproductive system development / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / intrinsic component of mitochondrial membrane / oxidoreductase activity, acting on NAD(P)H / mitochondrial processing peptidase complex / protein processing involved in protein targeting to mitochondrion / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respirasome assembly ...ubiquinone-6 biosynthetic process / reproductive system development / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / intrinsic component of mitochondrial membrane / oxidoreductase activity, acting on NAD(P)H / mitochondrial processing peptidase complex / protein processing involved in protein targeting to mitochondrion / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respirasome assembly / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / mitochondrial respiratory chain complex III assembly / NADH dehydrogenase activity / integral component of mitochondrial membrane / respiratory chain complex IV / mitochondrial respiratory chain complex I / mitochondrial large ribosomal subunit / protein lipoylation / mitochondrial respiratory chain complex III / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex I assembly / acyl carrier activity / mitochondrial electron transport, NADH to ubiquinone / acyl binding / quinol-cytochrome-c reductase / mitochondrial respirasome / multicellular organism aging / integral component of mitochondrial inner membrane / electron transport coupled proton transport / ubiquinol-cytochrome-c reductase activity / mitochondrial ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / cardiovascular system development / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / electron transport chain / ATP synthesis coupled electron transport / anterograde axonal transport / mitochondrial ATP synthesis coupled proton transport / cytochrome-c oxidase activity / cellular response to interferon-beta / ubiquinone binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrion morphogenesis / iron-sulfur cluster binding / mitochondrial electron transport, ubiquinol to cytochrome c / quinone binding / respiratory electron transport chain / chloroplast thylakoid membrane / enzyme regulator activity / respirasome / mitochondrial membrane / axon cytoplasm / aerobic respiration / reactive oxygen species metabolic process / extrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / central nervous system development / muscle contraction / fatty acid metabolic process / cellular response to retinoic acid / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / catalytic activity / mitochondrial intermembrane space / metalloendopeptidase activity / multicellular organism growth / negative regulation of cell growth / circadian rhythm / 4 iron, 4 sulfur cluster binding / NAD binding / FMN binding / mitochondrial inner membrane / oxidation-reduction process / response to oxidative stress / nuclear body / copper ion binding / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / heme binding / mitochondrion / membrane / integral component of membrane / nucleoplasm / plasma membrane / metal ion binding / cytosol / cytoplasm
Cupredoxin / Copper centre Cu(A) / Cytochrome c oxidase subunit I / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / Cytochrome c oxidase, subunit VIa / Peptidase M16, zinc-binding site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site ...Cupredoxin / Copper centre Cu(A) / Cytochrome c oxidase subunit I / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / Cytochrome c oxidase, subunit VIa / Peptidase M16, zinc-binding site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-quinone oxidoreductase subunit E-like / Cytochrome c oxidase, subunit Vb / Cytochrome c1 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase chain 4, N-terminal / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome c oxidase, subunit II / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-quinone oxidoreductase, chain G, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome b-c1 complex subunit 10 / Rieske iron-sulphur protein / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase subunit IV / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH ubiquinone oxidoreductase, F subunit / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase, subunit Va/VI / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NmrA-like domain / Molybdopterin oxidoreductase / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase, 4Fe-4S domain / Peptidase M16, C-terminal / Complex 1 LYR protein / Cytochrome b-c1 complex subunit 9 / Cytochrome C oxidase, subunit VIIB / Phosphopantetheine attachment site / NADH dehydrogenase subunit 5, C-terminal / Cytochrome c-like domain / Phosphopantetheine binding ACP domain / GRIM-19 / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Cytochrome c oxidase, subunit 8 / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome c oxidase, subunit VIb / Acyl carrier protein (ACP) / Cytochrome b-c1 complex, subunit 6 / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / Cytochrome c oxidase subunit VIIc / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit 6C / Cytochrome b-c1 complex subunit 8 / Cytochrome b/b6, N-terminal / Cytochrome b/b6, C-terminal / Rieske iron-sulphur protein, C-terminal / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome c oxidase, subunit VIa superfamily / NAD(P)-binding domain superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Thioredoxin-like superfamily / Cytochrome b/b6, C-terminal domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / ACP-like superfamily / Cytochrome c-like domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NuoE domain / NADH-quinone oxidoreductase subunit E, N-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / Cytochrome c oxidase subunit VII / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily
Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 7C, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial ...Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 7C, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 6C / NADH-ubiquinone oxidoreductase chain 4L / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 8B, mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase ubiquinone 1 beta subcomplex subunit 5, mitochondrial isoform 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH:ubiquinone oxidoreductase subunit A9 / Uncharacterized protein / AIF-MLS domain-containing protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase ubiquinone iron-sulfur protein 2, mitochondrial isoform 1 / Uncharacterized protein / Acyl carrier protein / NADH:ubiquinone oxidoreductase core subunit S1 / un:f1sif2: / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / CHCH domain-containing protein / NADH-ubiquinone oxidoreductase chain 1 / un:f1sly2: / Uncharacterized protein / un:f1srg2: / un:f1sty1: / Uncharacterized protein / Mitochondrial NADH dehydrogenase Fe-S protein 4 / NADH:ubiquinone oxidoreductase subunit B10 / NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 11 / Oxidored_q6 domain-containing protein / NADH:ubiquinone oxidoreductase subunit A1 / NADH:ubiquinone oxidoreductase subunit B9 / NADH-ubiquinone oxidoreductase chain 5
Biological speciesSus scrofa (pig) / Bovine (cattle) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsGu J / Wu M / Guo R / Yang M
CitationJournal: Nature / Year: 2016
Title: The architecture of the mammalian respirasome.
Authors: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang /
Abstract: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.
Validation ReportPDB-ID: 5gpn

SummaryFull reportAbout validation report
History
DepositionOct 31, 2016-
Header (metadata) releaseApr 5, 2017-
Map releaseApr 12, 2017-
UpdateApr 12, 2017-
Current statusApr 12, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5gpn
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9534.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 505.421 Å
1.05 Å/pix.
x 480 pix.
= 505.421 Å
1.05 Å/pix.
x 480 pix.
= 505.421 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05296 Å
Density
Contour LevelBy AUTHOR: 0.0216 / Movie #1: 0.0216
Minimum - Maximum-0.04734845 - 0.11140665
Average (Standard dev.)0.0005272059 (±0.003714595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 505.4208 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.05296041666671.05296041666671.0529604166667
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z505.421505.421505.421
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0470.1110.001

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Supplemental data

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Sample components

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Entire Respirasome

EntireName: Respirasome / Details: Mammalian, respirasome / Number of components: 74

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Component #1: protein, Respirasome

ProteinName: Respirasome / Details: Mammalian, respirasomeMammal / Recombinant expression: No
MassExperimental: 1.7 MDa
SourceSpecies: Sus scrofa (pig)

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Component #2: protein, Cytochrome b-c1 complex subunit 1, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 49.266254 kDa
SourceSpecies: Bovine (cattle)

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Component #3: protein, Cytochrome b-c1 complex subunit 2, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 46.575469 kDa
SourceSpecies: Bovine (cattle)

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Component #4: protein, Cytochrome b

ProteinName: Cytochrome b / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 42.62034 kDa
SourceSpecies: Bovine (cattle)

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Component #5: protein, Cytochrome c1, heme protein, mitochondrial

ProteinName: Cytochrome c1, heme protein, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.323277 kDa
SourceSpecies: Bovine (cattle)

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Component #6: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.572814 kDa
SourceSpecies: Bovine (cattle)

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Component #7: protein, Cytochrome b-c1 complex subunit 7

ProteinName: Cytochrome b-c1 complex subunit 7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.37119 kDa
SourceSpecies: Bovine (cattle)

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Component #8: protein, Cytochrome b-c1 complex subunit 8

ProteinName: Cytochrome b-c1 complex subunit 8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.606027 kDa
SourceSpecies: Bovine (cattle)

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Component #9: protein, Cytochrome b-c1 complex subunit 6, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 6, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.189116 kDa
SourceSpecies: Bovine (cattle)

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Component #10: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.964259 kDa
SourceSpecies: Bovine (cattle)

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Component #11: protein, Cytochrome b-c1 complex subunit 9

ProteinName: Cytochrome b-c1 complex subunit 9 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.209311 kDa
SourceSpecies: Bovine (cattle)

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Component #12: protein, Cytochrome b-c1 complex subunit 10

ProteinName: Cytochrome b-c1 complex subunit 10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.527604 kDa
SourceSpecies: Bovine (cattle)

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Component #13: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.241416 kDa
SourceSpecies: Pig (pig)

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Component #14: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.627398 kDa
SourceSpecies: Pig (pig)

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Component #15: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.552301 kDa
SourceSpecies: Pig (pig)

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Component #16: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.777742 kDa
SourceSpecies: Pig (pig)

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Component #17: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.893281 kDa
SourceSpecies: Pig (pig)

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Component #18: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.637766 kDa
SourceSpecies: Pig (pig)

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Component #19: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.439533 kDa
SourceSpecies: Pig (pig)

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Component #20: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.66752 kDa
SourceSpecies: Pig (pig)

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Component #21: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.077504 kDa
SourceSpecies: Pig (pig)

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Component #22: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.998448 kDa
SourceSpecies: Pig (pig)

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Component #23: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.859387 kDa
SourceSpecies: Pig (pig)

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Component #24: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.827253 kDa
SourceSpecies: Pig (pig)

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Component #25: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.6955 kDa
SourceSpecies: Pig (pig)

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Component #26: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 19.021332 kDa
SourceSpecies: Pig (pig)

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.225567 kDa
SourceSpecies: Pig (pig)

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Component #28: 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: 11.099798 kDa
SourceSpecies: Pig (pig)

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Component #29: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.506591 kDa
SourceSpecies: Pig (pig)

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Component #30: 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: 42.606324 kDa
SourceSpecies: Pig (pig)

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Component #31: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 40.476082 kDa
SourceSpecies: Pig (pig)

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Component #32: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.911611 kDa
SourceSpecies: Pig (pig)

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Component #33: protein, Acyl carrier protein

ProteinName: Acyl carrier protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.326223 kDa
SourceSpecies: Pig (pig)

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Component #34: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.587006 kDa
SourceSpecies: Pig (pig)

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Component #35: protein, Mitochondrial NADH dehydrogenase Fe-S protein 4

ProteinName: Mitochondrial NADH dehydrogenase Fe-S protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.7185 kDa
SourceSpecies: Pig (pig)

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Component #36: 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: 13.34895 kDa
SourceSpecies: Pig (pig)

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Component #37: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.9436 kDa
SourceSpecies: Bovine (cattle)

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Component #38: protein, Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.179646 kDa
SourceSpecies: Bovine (cattle)

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Component #39: protein, Cytochrome c oxidase subunit 5A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5A, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.453081 kDa
SourceSpecies: Bovine (cattle)

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Component #40: protein, Cytochrome c oxidase subunit 5B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5B, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.684038 kDa
SourceSpecies: Bovine (cattle)

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Component #41: protein, Cytochrome c oxidase subunit 6A2, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6A2, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.452687 kDa
SourceSpecies: Bovine (cattle)

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Component #42: protein, Cytochrome c oxidase subunit 6B1

ProteinName: Cytochrome c oxidase subunit 6B1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.039244 kDa
SourceSpecies: Bovine (cattle)

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Component #43: protein, Cytochrome c oxidase subunit 6C

ProteinName: Cytochrome c oxidase subunit 6C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.494982 kDa
SourceSpecies: Bovine (cattle)

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Component #44: protein, Cytochrome c oxidase subunit 7A1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7A1, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.682726 kDa
SourceSpecies: Bovine (cattle)

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Component #45: protein, Cytochrome c oxidase subunit 7B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7B, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.365217 kDa
SourceSpecies: Bovine (cattle)

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Component #46: protein, Cytochrome c oxidase subunit 7C, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7C, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.449396 kDa
SourceSpecies: Bovine (cattle)

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Component #47: protein, Cytochrome c oxidase subunit 8B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 8B, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.967756 kDa
SourceSpecies: Bovine (cattle)

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Component #48: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.065844 kDa
SourceSpecies: Bovine (cattle)

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Component #49: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.040393 kDa
SourceSpecies: Bovine (cattle)

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Component #50: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.422071 kDa
SourceSpecies: Pig (pig)

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Component #51: 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: 8.088424 kDa
SourceSpecies: Pig (pig)

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Component #52: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 3.677524 kDa
SourceSpecies: Pig (pig)

+
Component #53: 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: 13.32159 kDa
SourceSpecies: Pig (pig)

+
Component #54: 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: 14.953313 kDa
SourceSpecies: Pig (pig)

+
Component #55: 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: 14.686894 kDa
SourceSpecies: Pig (pig)

+
Component #56: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.944768 kDa
SourceSpecies: Pig (pig)

+
Component #57: 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: 21.733711 kDa
SourceSpecies: Pig (pig)

+
Component #58: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.327655 kDa
SourceSpecies: Pig (pig)

+
Component #59: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.630037 kDa
SourceSpecies: Pig (pig)

+
Component #60: 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: 20.064096 kDa
SourceSpecies: Pig (pig)

+
Component #61: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.485986 kDa
SourceSpecies: Pig (pig)

+
Component #62: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.91158 kDa
SourceSpecies: Pig (pig)

+
Component #63: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.464797 kDa
SourceSpecies: Pig (pig)

+
Component #64: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.124378 kDa
SourceSpecies: Pig (pig)

+
Component #65: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

+
Component #66: ligand, HEME C

LigandName: HEME C / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.618503 kDa

+
Component #67: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

+
Component #68: ligand, IRON/SULFUR CLUSTER

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

+
Component #69: ligand, FLAVIN MONONUCLEOTIDE

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

+
Component #70: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

+
Component #71: ligand, ZINC ION

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

+
Component #72: ligand, HEME-A

LigandName: HEME-A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.852837 kDa

+
Component #73: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

+
Component #74: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationCryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 139996
3D reconstructionSoftware: EMAN / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
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