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- EMDB-10848: Cytochrome c oxidase from Saccharomyces cerevisiae -

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Basic information

Entry
Database: EMDB / ID: EMD-10848
TitleCytochrome c oxidase from Saccharomyces cerevisiae
Map data
Sample
  • Complex: Cytochrome c oxidase
    • Protein or peptide: x 12 types
  • Ligand: x 7 types
KeywordsCIV / CytcO / ELECTRON TRANSPORT
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / electron transport coupled proton transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / proton transmembrane transport / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / zinc ion binding / metal ion binding
Similarity search - Function
Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily ...Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxin
Similarity search - Domain/homology
Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial ...Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 26, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsBerndtsson J / Rathore S / Ott M
Funding support Sweden, 4 items
OrganizationGrant numberCountry
Swedish Research Council2014-4116 Sweden
Swedish Research Council2018-03694 Sweden
Knut and Alice Wallenberg Foundation2017.0091 Sweden
Knut and Alice Wallenberg Foundation2013.0006 Sweden
CitationJournal: EMBO Rep / Year: 2020
Title: Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance.
Authors: Jens Berndtsson / Andreas Kohler / Sorbhi Rathore / Lorena Marin-Buera / Hannah Dawitz / Jutta Diessl / Verena Kohler / Antoni Barrientos / Sabrina Büttner / Flavia Fontanesi / Martin Ott /
Abstract: Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in ...Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms.
History
DepositionApr 10, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ymy
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10848.png

Downloads & links

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Map

FileDownload / File: emd_10848.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41 / Movie #1: 0.41
Minimum - Maximum-1.2105628 - 2.4105902
Average (Standard dev.)0.004612802 (±0.058248185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 392.2 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-1.2112.4110.005

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Supplemental data

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Mask #1

Fileemd_10848_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_10848_half_map_1.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Fist half map

Fileemd_10848_half_map_2.map
AnnotationFist half map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cytochrome c oxidase

EntireName: Cytochrome c oxidase
Components
  • Complex: Cytochrome c oxidase
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 4, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5A, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 9, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 12, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 13, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 26, mitochondrial
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (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
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: ZINC ION

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Supramolecule #1: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: W303-1b / Organelle: Mitochondria

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Macromolecule #1: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 58.316938 KDa
SequenceString: WLYSTNAKDI AVLYFMLAIF SGMAGTAMSL IIRLELAAPG SQYLHGNSQL FNVLVVGHAV LMIFFLVMPA LIGGFGNYLL PLMIGATDT AFPRINNIAF WVLPMGLVCL VTSTLVESGA GTGWTVYPPL SSIQAHSGPS VDLAIFALHL TSISSLLGAI N FIVTTLNM ...String:
WLYSTNAKDI AVLYFMLAIF SGMAGTAMSL IIRLELAAPG SQYLHGNSQL FNVLVVGHAV LMIFFLVMPA LIGGFGNYLL PLMIGATDT AFPRINNIAF WVLPMGLVCL VTSTLVESGA GTGWTVYPPL SSIQAHSGPS VDLAIFALHL TSISSLLGAI N FIVTTLNM RTNGMTMHKL PLFVWSIFIT AFLLLLSLPV LSAGITMLLL DRNFNTSFFE VSGGGDPILY EHLFWFFGHP EV YILIIPG FGIISHVVST YSKKPVFGEI SMVYAMASIG LLGFLVWSHH MYIVGLDADT RAYFTSATMI IAIPTGIKIF SWL ATIHGG SIRLATPMLY AIAFLFLFTM GGLTGVALAN ASLDVAFHDT YYVVGHFHYV LSMGAIFSLF AGYYYWSPQI LGLN YNEKL AQIQFWLIFI GANVIFFPMH FLGINGMPRR IPDYPDAFAG WNYVASIGSF IATLSLFLFI YILYDQLVNG LNNKV NNKS VIYNKAPDFV ESNTIFNLNT VKSSSIEFLL TSPPAVHSFN TPAVQS

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #2: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 26.779816 KDa
SequenceString: DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYTIVMTY SKNPIAYKYI KHGQTIEVIW TIFPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGYQW YWKYEYSDFI NDSGETVEFE SYVIPDELLE EGQLRLLDTD TSMVVPVDTH I RFVVTAAD ...String:
DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYTIVMTY SKNPIAYKYI KHGQTIEVIW TIFPAVILLI IAFPSFILL YLCDEVISPA MTIKAIGYQW YWKYEYSDFI NDSGETVEFE SYVIPDELLE EGQLRLLDTD TSMVVPVDTH I RFVVTAAD VIHDFAIPSL GIKVDATPGR LNQVSALIQR EGVFYGACSE LCGTGHANMP IKIEAVSLPK FLEWLNEQ

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #3: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 30.252391 KDa
SequenceString: THLERSRHQQ HPFHMVMPSP WPIVVSFALL SLALSTALTM HGYIGNMNMV YLALFVLLTS SILWFRDIVA EATYLGDHTM AVRKGINLG FLMFVLSEVL IFAGLFWAYF HSAMSPDVTL GACWPPVGIE AVQPTELPLL NTIILLSSGA TVTYSHHALI A GNRNKALS ...String:
THLERSRHQQ HPFHMVMPSP WPIVVSFALL SLALSTALTM HGYIGNMNMV YLALFVLLTS SILWFRDIVA EATYLGDHTM AVRKGINLG FLMFVLSEVL IFAGLFWAYF HSAMSPDVTL GACWPPVGIE AVQPTELPLL NTIILLSSGA TVTYSHHALI A GNRNKALS GLLITFWLIV IFVTCQYIEY TNAAFTISDG VYGSVFYAGT GLHFLHMVML AAMLGVNYWR MRNYHLTAGH HV GYETTII YTHVLDVIWL FLYVVFYWWG V

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #4: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 12.694382 KDa
SequenceString:
VVKTAQNLAE VNGPETLIGP GAKEGTVPTD LDQETGLARL ELLGKLEGID VFDTKPLDSS RKGTMKDPII IESYDDYRYV GCTGSPAGS HTIMWLKPTV NEVARCWECG SVYKLNPV

UniProtKB: Cytochrome c oxidase subunit 4, mitochondrial

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Macromolecule #5: Cytochrome c oxidase subunit 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 14.324147 KDa
SequenceString:
ALSNAAVMDL QSRWENMPST EQQDIVSKLS ERQKLPWAQL TEPEKQAVWY ISYGEWGPRR PVLNKGDSSF IAKGVAAGLL FSVGLFAVV RMAGGQDAKT MNKEWQLKSD EYLKSKNANP WGGYSQVQS

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

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Macromolecule #6: Cytochrome c oxidase subunit 6, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 11.725173 KDa
SequenceString:
ETFEEFTARY EKEFDEAYDL FEVQRVLNNC FSYDLVPAPA VIEKALRAAR RVNDLPTAIR VFEALKYKVE NEDQYKAYLD ELKDVRQEL GVPLKEELFP

UniProtKB: Cytochrome c oxidase subunit 6, mitochondrial

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Macromolecule #7: Cytochrome c oxidase subunit 7, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 6.410639 KDa
SequenceString:
NKVIQLQKIF QSSTKPLWWR HPRSALYLYP FYAIFAVAVV TPLLYIPNAI RGIKA

UniProtKB: Cytochrome c oxidase subunit 7, mitochondrial

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Macromolecule #8: Cytochrome c oxidase subunit 8, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 5.737735 KDa
SequenceString:
VHFKDGVYEN IPFKVKGRKT PYALSHFGFF AIGFAVPFVA CYVQLKKSGA F

UniProtKB: Cytochrome c oxidase subunit 8, mitochondrial

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Macromolecule #9: Cytochrome c oxidase subunit 9, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 9, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 6.056131 KDa
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AE

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

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Macromolecule #10: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 9.225291 KDa
SequenceString:
NSPLHTVGFD ARFPQQNQTK HCWQSYVDYH KCVNMKGEDF APCKVFWKTY NALCPLDWIE KWDDQREKGI FAGDINSD

UniProtKB: Cytochrome c oxidase subunit 12, mitochondrial

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Macromolecule #11: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 13.306061 KDa
SequenceString:
NALKPAFGPP DKVAAQKFKE SLMATEKHAK DTSNMWVKIS VWVALPAIAL TAVNTYFVEK EHAEHREHLK HVPDSEWPRD YEFMNIRSK PFFWGDGDKT LFWNPVVNRH IEHDD

UniProtKB: Cytochrome c oxidase subunit 13, mitochondrial

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Macromolecule #12: Cytochrome c oxidase subunit 26, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 26, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 4.347023 KDa
SequenceString:
ESWVITEGRR LIPEIFQWSA VLSVCLGWPG AVYFFSKA

UniProtKB: Cytochrome c oxidase subunit 26, mitochondrial

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Macromolecule #13: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #14: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 14 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #15: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 15 / Number of copies: 7 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #16: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16...

MacromoleculeName: (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
type: ligand / ID: 16 / Number of copies: 1 / Formula: CN3
Molecular weightTheoretical: 834.862 Da
Chemical component information

ChemComp-CN3:
(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

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Macromolecule #17: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #18: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 18 / Number of copies: 3 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
0.1 %C56H92O29Digitonin
1.0 mMC7H7FO2Sphenylmethylsulfonyl fluoride
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 8775 / Average exposure time: 9.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.0014 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 647805
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 201223
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2) / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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