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- EMDB-9539: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -

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Entry
Database: EMDB / ID: 9539
TitleCryo-EM structure of mammalian respiratory supercomplex I1III2IV1
Map data
SampleRespiratory supercomplex I1III2IV1
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • Acyl carrier protein, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • (ligand) x 14
Function / homologyNADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Rieske iron-sulphur protein / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 ...NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Rieske iron-sulphur protein / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Rieske [2Fe-2S] iron-sulphur domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Peptidase M16, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Phosphopantetheine binding ACP domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase, 4Fe-4S domain / Ribosomal protein/NADH dehydrogenase domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Peptidase M16, C-terminal / Complex 1 LYR protein / Cytochrome b-c1 complex subunit 9 / NmrA-like domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase subunit 5, C-terminal / Globular protein, non-globular alpha/beta subunit / Metalloenzyme, LuxS/M16 peptidase-like / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NAD(P)H-quinone oxidoreductase subunit D/H / UcrQ family / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6/petB / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Rieske [2Fe-2S] domain / Proton-conducting membrane transporter / Molybdopterin oxidoreductase / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-quinone oxidoreductase, subunit D superfamily / Phosphopantetheine attachment site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Insulinase (Peptidase family M16) / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Deoxynucleoside kinase / Cytochrome c oxidase subunit Va / Ubiquinol-cytochrome C reductase hinge protein / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Protein MGARP / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Cytochrome b/b6-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Single alpha-helix domain superfamily / Cytochrome b / Deoxynucleoside kinase domain / Protein MGARP, N-terminal / Cytochrome b/b6, C-terminal domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / ACP-like superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain superfamily / Molybdopterin oxidoreductase / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Phosphopantetheine attachment site / Zinc-finger domain / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Mitochondria Localisation Sequence
Function and homology information
SourceSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsGu J / Wu M
CitationJournal: Cell / Year: 2016
Title: Structure of Mammalian Respiratory Supercomplex IIIIIV.
Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang
Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.
Validation ReportPDB-ID: 5gup

SummaryFull reportAbout validation report
DateDeposition: Aug 30, 2016 / Header (metadata) release: Mar 29, 2017 / Map release: Mar 29, 2017 / Last update: Mar 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0504
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0504
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5gup
  • Surface level: 0.0504
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9539.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.08 Å/pix.
= 518.4 Å
480 pix
1.08 Å/pix.
= 518.4 Å
480 pix
1.08 Å/pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour Level:0.0504 (by author), 0.0504 (movie #1):
Minimum - Maximum-0.12587553 - 0.51883394
Average (Standard dev.)0.0008468492 (0.0067121573)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ399399399
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1260.5190.001

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Supplemental data

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Sample components

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Entire Respiratory supercomplex I1III2IV1

EntireName: Respiratory supercomplex I1III2IV1 / Details: Supercomplex generated by complex I, III and IV. / Number of components: 82
MassExperimental: 1.7 MDa

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Component #1: protein, Respiratory supercomplex I1III2IV1

ProteinName: Respiratory supercomplex I1III2IV1 / Details: Supercomplex generated by complex I, III and IV. / Recombinant expression: No
MassExperimental: 1.7 MDa
SourceSpecies: Sus scrofa (pig)

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Component #2: protein, Cytochrome c oxidase subunit 6C

ProteinName: Cytochrome c oxidase subunit 6C / Recombinant expression: No
MassTheoretical: 8.494982 kDa
SourceSpecies: Sus scrofa (pig)

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Component #3: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Recombinant expression: No
MassTheoretical: 50.637766 kDa
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Recombinant expression: No
MassTheoretical: 52.552301 kDa
SourceSpecies: Sus scrofa (pig)

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Component #5: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Recombinant expression: No
MassTheoretical: 30.241416 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Recombinant expression: No
MassTheoretical: 26.301637 kDa
SourceSpecies: Sus scrofa (pig)

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Component #7: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Recombinant expression: No
MassTheoretical: 13.34895 kDa
SourceSpecies: Sus scrofa (pig)

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Component #8: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
Recombinant expression: No
MassTheoretical: 79.627398 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Recombinant expression: No
MassTheoretical: 23.893281 kDa
SourceSpecies: Sus scrofa (pig)

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Component #10: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Recombinant expression: No
MassTheoretical: 23.777742 kDa
SourceSpecies: Sus scrofa (pig)

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Component #11: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Recombinant expression: No
MassTheoretical: 19.7185 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Recombinant expression: No
MassTheoretical: 17.162439 kDa
SourceSpecies: Sus scrofa (pig)

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Component #13: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Recombinant expression: No
MassTheoretical: 42.606324 kDa
SourceSpecies: Sus scrofa (pig)

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Component #14: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Recombinant expression: No
MassTheoretical: 12.64859 kDa
SourceSpecies: Sus scrofa (pig)

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Component #15: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Recombinant expression: No
MassTheoretical: 13.32159 kDa
SourceSpecies: Sus scrofa (pig)

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Component #16: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Recombinant expression: No
MassTheoretical: 17.326223 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Recombinant expression: No
MassTheoretical: 11.099798 kDa
SourceSpecies: Sus scrofa (pig)

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Component #18: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 14.953313 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 8.088424 kDa
SourceSpecies: Sus scrofa (pig)

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Component #20: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Recombinant expression: No
MassTheoretical: 9.225567 kDa
SourceSpecies: Sus scrofa (pig)

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Component #21: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Recombinant expression: No
MassTheoretical: 40.476082 kDa
SourceSpecies: Sus scrofa (pig)

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Component #22: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Recombinant expression: No
MassTheoretical: 14.686894 kDa
SourceSpecies: Sus scrofa (pig)

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Component #23: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Recombinant expression: No
MassTheoretical: 16.911611 kDa
SourceSpecies: Sus scrofa (pig)

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Component #24: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Recombinant expression: No
MassTheoretical: 11.939366 kDa
SourceSpecies: Sus scrofa (pig)

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Component #25: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
Recombinant expression: No
MassTheoretical: 11.128515 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Recombinant expression: No
MassTheoretical: 21.587006 kDa
SourceSpecies: Sus scrofa (pig)

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 15.603177 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Recombinant expression: No
MassTheoretical: 21.702543 kDa
SourceSpecies: Sus scrofa (pig)

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Component #29: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Recombinant expression: No
MassTheoretical: 20.944768 kDa
SourceSpecies: Sus scrofa (pig)

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Recombinant expression: No
MassTheoretical: 17.384729 kDa
SourceSpecies: Sus scrofa (pig)

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Component #31: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Recombinant expression: No
MassTheoretical: 8.630037 kDa
SourceSpecies: Sus scrofa (pig)

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Component #32: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / Recombinant expression: No
MassTheoretical: 14.327655 kDa
SourceSpecies: Sus scrofa (pig)

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Component #33: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Recombinant expression: No
MassTheoretical: 12.506591 kDa
SourceSpecies: Sus scrofa (pig)

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Component #34: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Recombinant expression: No
MassTheoretical: 39.077504 kDa
SourceSpecies: Sus scrofa (pig)

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Component #35: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Recombinant expression: No
MassTheoretical: 12.998448 kDa
SourceSpecies: Sus scrofa (pig)

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Component #36: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Recombinant expression: No
MassTheoretical: 10.827253 kDa
SourceSpecies: Sus scrofa (pig)

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Component #37: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Recombinant expression: No
MassTheoretical: 68.6955 kDa
SourceSpecies: Sus scrofa (pig)

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Component #38: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Recombinant expression: No
MassTheoretical: 19.021332 kDa
SourceSpecies: Sus scrofa (pig)

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 7.044278 kDa
SourceSpecies: Sus scrofa (pig)

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Component #40: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Recombinant expression: No
MassTheoretical: 15.11735 kDa
SourceSpecies: Sus scrofa (pig)

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Component #41: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Recombinant expression: No
MassTheoretical: 21.864906 kDa
SourceSpecies: Sus scrofa (pig)

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Component #42: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Recombinant expression: No
MassTheoretical: 51.859387 kDa
SourceSpecies: Sus scrofa (pig)

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Component #43: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Recombinant expression: No
MassTheoretical: 35.66752 kDa
SourceSpecies: Sus scrofa (pig)

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Component #44: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Recombinant expression: No
MassTheoretical: 20.064096 kDa
SourceSpecies: Sus scrofa (pig)

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Component #45: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Recombinant expression: No
MassTheoretical: 16.487887 kDa
SourceSpecies: Sus scrofa (pig)

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Component #46: protein, Cytochrome b-c1 complex subunit 1, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Recombinant expression: No
MassTheoretical: 52.75632 kDa
SourceSpecies: Sus scrofa (pig)

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Component #47: protein, Cytochrome b-c1 complex subunit 2, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrial / Recombinant expression: No
MassTheoretical: 48.264477 kDa
SourceSpecies: Sus scrofa (pig)

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Component #48: protein, Cytochrome b

ProteinName: Cytochrome b / Recombinant expression: No
MassTheoretical: 42.840715 kDa
SourceSpecies: Sus scrofa (pig)

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Component #49: protein, Cytochrome c1, heme protein, mitochondrial

ProteinName: Cytochrome c1, heme protein, mitochondrial / Recombinant expression: No
MassTheoretical: 35.48893 kDa
SourceSpecies: Sus scrofa (pig)

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Component #50: protein, Cytochrome b-c1 complex subunit 7

ProteinName: Cytochrome b-c1 complex subunit 7 / Recombinant expression: No
MassTheoretical: 13.587549 kDa
SourceSpecies: Sus scrofa (pig)

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Component #51: protein, Cytochrome b-c1 complex subunit 8

ProteinName: Cytochrome b-c1 complex subunit 8 / Recombinant expression: No
MassTheoretical: 9.784339 kDa
SourceSpecies: Sus scrofa (pig)

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Component #52: protein, Cytochrome b-c1 complex subunit 6, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 6, mitochondrial / Recombinant expression: No
MassTheoretical: 10.685803 kDa
SourceSpecies: Sus scrofa (pig)

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Component #53: protein, Cytochrome b-c1 complex subunit 9

ProteinName: Cytochrome b-c1 complex subunit 9 / Recombinant expression: No
MassTheoretical: 7.41253 kDa
SourceSpecies: Sus scrofa (pig)

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Component #54: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Recombinant expression: No
MassTheoretical: 29.4926 kDa
SourceSpecies: Sus scrofa (pig)

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Component #55: protein, Cytochrome b-c1 complex subunit 10

ProteinName: Cytochrome b-c1 complex subunit 10 / Recombinant expression: No
MassTheoretical: 6.560654 kDa
SourceSpecies: Sus scrofa (pig)

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Component #56: protein, Cytochrome b-c1 complex subunit Rieske transit peptide, ...

ProteinName: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Recombinant expression: No
MassTheoretical: 7.900107 kDa
SourceSpecies: Sus scrofa (pig)

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Component #57: protein, Cytochrome c oxidase subunit 8B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 8B, mitochondrial / Recombinant expression: No
MassTheoretical: 4.967756 kDa
SourceSpecies: Sus scrofa (pig)

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Component #58: protein, Cytochrome c oxidase subunit 7A1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7A1, mitochondrial / Recombinant expression: No
MassTheoretical: 6.682726 kDa
SourceSpecies: Sus scrofa (pig)

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Component #59: protein, Cytochrome c oxidase subunit 7B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7B, mitochondrial / Recombinant expression: No
MassTheoretical: 6.365217 kDa
SourceSpecies: Sus scrofa (pig)

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Component #60: protein, Cytochrome c oxidase subunit 7C, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7C, mitochondrial / Recombinant expression: No
MassTheoretical: 5.449396 kDa
SourceSpecies: Sus scrofa (pig)

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Component #61: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Recombinant expression: No
MassTheoretical: 57.065844 kDa
SourceSpecies: Sus scrofa (pig)

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Component #62: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Recombinant expression: No
MassTheoretical: 26.040393 kDa
SourceSpecies: Sus scrofa (pig)

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Component #63: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Recombinant expression: No
MassTheoretical: 29.9436 kDa
SourceSpecies: Sus scrofa (pig)

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Component #64: protein, Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Recombinant expression: No
MassTheoretical: 17.179646 kDa
SourceSpecies: Sus scrofa (pig)

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Component #65: protein, Cytochrome c oxidase subunit 5A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5A, mitochondrial / Recombinant expression: No
MassTheoretical: 12.453081 kDa
SourceSpecies: Sus scrofa (pig)

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Component #66: protein, Cytochrome c oxidase subunit 5B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5B, mitochondrial / Recombinant expression: No
MassTheoretical: 10.684038 kDa
SourceSpecies: Sus scrofa (pig)

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Component #67: protein, Cytochrome c oxidase subunit 6A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6A, mitochondrial / Recombinant expression: No
MassTheoretical: 9.452687 kDa
SourceSpecies: Sus scrofa (pig)

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Component #68: protein, Cytochrome c oxidase subunit 6B1

ProteinName: Cytochrome c oxidase subunit 6B1 / Recombinant expression: No
MassTheoretical: 10.039244 kDa
SourceSpecies: Sus scrofa (pig)

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Component #69: ligand, IRON/SULFUR CLUSTER

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

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Component #70: ligand, FLAVIN MONONUCLEOTIDE

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

+
Component #71: ligand, FE2/S2 (INORGANIC) CLUSTER

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

+
Component #72: ligand, (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIM...

LigandName: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.767132 kDa

+
Component #73: 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 #74: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

+
Component #75: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

+
Component #76: ligand, 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

LigandName: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.749073 kDa

+
Component #77: ligand, PROTOPORPHYRIN IX CONTAINING FE

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

+
Component #78: ligand, HEME C

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

+
Component #79: ligand, HEME-A

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

+
Component #80: ligand, COPPER (II) ION

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

+
Component #81: ligand, MAGNESIUM ION

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

+
Component #82: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE / 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: 1.25 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 161912
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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About Yorodumi

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Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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