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- EMDB-0004: Saccharomyces cerevisiae respiratory supercomplex III2IV -

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Basic information

Entry
Database: EMDB / ID: EMD-0004
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Map data
SampleSaccharomyces cerevisiae Supercomplex (III2IV)
  • (Saccharomyces cerevisiae complex ...) x 2
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • (Cytochrome c oxidase subunit ...) x 9
  • (Cytochrome c oxidase polypeptide ...) x 2
  • Unknown Cox subunit
  • (ligand) x 13
Function / homology
Function and homology information


mitochondrial crista / mitochondrial respiratory chain complex IV assembly / 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 / oxidoreduction-driven active transmembrane transporter activity / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respirasome ...mitochondrial crista / mitochondrial respiratory chain complex IV assembly / 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 / oxidoreduction-driven active transmembrane transporter activity / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respirasome / quinol-cytochrome-c reductase / oxidative phosphorylation / integral component of mitochondrial inner membrane / electron transport coupled proton transport / ubiquinol-cytochrome-c reductase activity / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / electron transport chain / ATP synthesis coupled electron transport / mitochondrial ATP synthesis coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / enzyme regulator activity / aerobic respiration / nuclear periphery / 2 iron, 2 sulfur cluster binding / catalytic activity / mitochondrial intermembrane space / metalloendopeptidase activity / mitochondrial inner membrane / copper ion binding / electron transfer activity / heme binding / mitochondrion / zinc ion binding / integral component of membrane / plasma membrane / metal ion binding / cytosol
Cupredoxin / Cytochrome c oxidase, subunit VIb / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit Va/VI ...Cupredoxin / Cytochrome c oxidase, subunit VIb / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit Va/VI / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c1 / Cytochrome c oxidase, subunit Vb / Copper centre Cu(A) / Peptidase M16, zinc-binding site / Cytochrome c oxidase, subunit VIa / Rieske iron-sulphur protein, C-terminal / Peptidase M16, C-terminal / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit VIIa, fungal / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase, subunit VIa, conserved site / Rieske [2Fe-2S] iron-sulphur domain / Di-haem cytochrome, transmembrane / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome b-c1 complex subunit 9 / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VII / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase-like, subunit I superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain 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 III / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit III domain / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6-like domain superfamily / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit I domain
Cytochrome c oxidase subunit 7A / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 6A, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 7 / 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 / Cytochrome c oxidase subunit 2 ...Cytochrome c oxidase subunit 7A / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 6A, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 7 / 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 / Cytochrome c oxidase subunit 2 / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase polypeptide VIII, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase polypeptide 5A, mitochondrial / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome b / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 6B
Biological speciesSaccharomyces cerevisiae W303 (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsRathore S / Berndtsson J / Conrad J / Ott M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott /
Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
Validation ReportPDB-ID: 6giq

SummaryFull reportAbout validation report
History
DepositionMay 15, 2018-
Header (metadata) releaseJul 18, 2018-
Map releaseJan 2, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6giq
  • Surface level: 0.33
  • 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_0004.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 370 pix.
= 392.2 Å
1.06 Å/pix.
x 370 pix.
= 392.2 Å
1.06 Å/pix.
x 370 pix.
= 392.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.4
Minimum - Maximum-1.2225217 - 2.422639
Average (Standard dev.)0.008202017 (±0.08052676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-1.2232.4230.008

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Supplemental data

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Half map: Halfmap1

Fileemd_0004_half_map_1.map
AnnotationHalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Halfmap2

Fileemd_0004_half_map_2.map
AnnotationHalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Saccharomyces cerevisiae Supercomplex (III2IV)

EntireName: Saccharomyces cerevisiae Supercomplex (III2IV) / Number of components: 38

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Component #1: protein, Saccharomyces cerevisiae Supercomplex (III2IV)

ProteinName: Saccharomyces cerevisiae Supercomplex (III2IV) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Component #2: protein, Saccharomyces cerevisiae complex III

ProteinName: Saccharomyces cerevisiae complex III / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Component #3: protein, Saccharomyces cerevisiae complex IV

ProteinName: Saccharomyces cerevisiae complex IV / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Component #4: protein, Cytochrome b-c1 complex subunit 1, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 50.282594 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Cytochrome b-c1 complex subunit 2, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 40.528008 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, Cytochrome b

ProteinName: Cytochrome b / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.68659 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, Cytochrome c1, heme protein, mitochondrial

ProteinName: Cytochrome c1, heme protein, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.097523 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.393973 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.276074 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, Cytochrome b-c1 complex subunit 7

ProteinName: Cytochrome b-c1 complex subunit 7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.583755 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, Cytochrome b-c1 complex subunit 8

ProteinName: Cytochrome b-c1 complex subunit 8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.987511 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, Cytochrome b-c1 complex subunit 9

ProteinName: Cytochrome b-c1 complex subunit 9 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.485334 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, Cytochrome b-c1 complex subunit 10

ProteinName: Cytochrome b-c1 complex subunit 10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.602913 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.832586 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.585055 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.383582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, Cytochrome c oxidase subunit 4, mitochondrial

ProteinName: Cytochrome c oxidase subunit 4, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.164557 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, Cytochrome c oxidase polypeptide 5A, mitochondrial

ProteinName: Cytochrome c oxidase polypeptide 5A, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.161465 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, Cytochrome c oxidase subunit 6, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.3666 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, Cytochrome c oxidase subunit 7

ProteinName: Cytochrome c oxidase subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.942349 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, Cytochrome c oxidase polypeptide VIII, mitochondrial

ProteinName: Cytochrome c oxidase polypeptide VIII, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.921686 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, Cytochrome c oxidase subunit 7A

ProteinName: Cytochrome c oxidase subunit 7A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.974226 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, Cytochrome c oxidase subunit 6B

ProteinName: Cytochrome c oxidase subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.799895 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, Cytochrome c oxidase subunit 6A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6A, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.046146 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, Unknown Cox subunit

ProteinName: Unknown Cox subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.656265 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: ligand, (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pen...

LigandName: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.592785 kDa

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Component #27: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #28: ligand, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(t...

LigandName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.691959 kDa

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Component #29: ligand, (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,...

LigandName: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.634631 kDa

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Component #30: ligand, 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-H...

LigandName: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.592891 kDa

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Component #31: ligand, (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetr...

LigandName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.564732 kDa

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Component #32: ligand, FE2/S2 (INORGANIC) CLUSTER

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

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Component #33: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.734039 kDa

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Component #34: ligand, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(...

LigandName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.593773 kDa

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Component #35: ligand, (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-di...

LigandName: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.834862 kDa

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Component #36: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

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Component #37: ligand, HEME-A

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

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Component #38: ligand, DINUCLEAR COPPER ION

LigandName: DINUCLEAR COPPER ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.127092 kDa

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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

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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 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 203271
3D reconstructionSoftware: cryoSPARC / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Cross-Correlation coefficient / Refinement space: REAL
Output model

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