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- EMDB-27196: Mammalian CIV with GDN bound -

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Basic information

Entry
Database: EMDB / ID: EMD-27196
TitleMammalian CIV with GDN bound
Map data
Sample
  • Complex: Cytochrome c oxidase
    • Protein or peptide: x 13 types
  • Ligand: x 8 types
Keywordsmitochondrial electron transport chain / inhibitor / complex IV / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB ...Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, 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 VIb superfamily / 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 2, C-terminal / Cytochrome oxidase c subunit VIb / 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 Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / 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 II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 3 / 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 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial ...Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / 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 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDi Trani J / Rubinstein J
Funding support Canada, Sweden, 4 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Knut and Alice Wallenberg Foundation2019.0043 Sweden
Swedish Research Council2018-04619 Sweden
Swedish Research Council016-07213 Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural basis of mammalian complex IV inhibition by steroids.
Authors: Justin M Di Trani / Agnes Moe / Daniel Riepl / Patricia Saura / Ville R I Kaila / Peter Brzezinski / John L Rubinstein /
Abstract: The mitochondrial electron transport chain maintains the proton motive force that powers adenosine triphosphate (ATP) synthesis. The energy for this process comes from oxidation of reduced ...The mitochondrial electron transport chain maintains the proton motive force that powers adenosine triphosphate (ATP) synthesis. The energy for this process comes from oxidation of reduced nicotinamide adenine dinucleotide (NADH) and succinate, with the electrons from this oxidation passed via intermediate carriers to oxygen. Complex IV (CIV), the terminal oxidase, transfers electrons from the intermediate electron carrier cytochrome to oxygen, contributing to the proton motive force in the process. Within CIV, protons move through the K and D pathways during turnover. The former is responsible for transferring two protons to the enzyme's catalytic site upon its reduction, where they eventually combine with oxygen and electrons to form water. CIV is the main site for respiratory regulation, and although previous studies showed that steroid binding can regulate CIV activity, little is known about how this regulation occurs. Here, we characterize the interaction between CIV and steroids using a combination of kinetic experiments, structure determination, and molecular simulations. We show that molecules with a sterol moiety, such as glyco-diosgenin and cholesteryl hemisuccinate, reversibly inhibit CIV. Flash photolysis experiments probing the rapid equilibration of electrons within CIV demonstrate that binding of these molecules inhibits proton uptake through the K pathway. Single particle cryogenic electron microscopy (cryo-EM) of CIV with glyco-diosgenin reveals a previously undescribed steroid binding site adjacent to the K pathway, and molecular simulations suggest that the steroid binding modulates the conformational dynamics of key residues and proton transfer kinetics within this pathway. The binding pose of the sterol group sheds light on possible structural gating mechanisms in the CIV catalytic cycle.
History
DepositionJun 2, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27196.png

Downloads & links

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Map

FileDownload / File: emd_27196.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.07
Minimum - Maximum-5.290759 - 7.6107597
Average (Standard dev.)-0.0006033711 (±0.23865974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27196_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #1

Fileemd_27196_half_map_2.map
Projections & Slices
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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 isoform 1, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5A, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6A2, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 6B1
    • Protein or peptide: Cytochrome c oxidase subunit 6C
    • Protein or peptide: Cytochrome c oxidase subunit 7A1, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7B, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7C, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8A, mitochondrial
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM ION
  • Ligand: HEME-A
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • 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-#13
Source (natural)Organism: Bos taurus (domestic cattle)

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 56.964672 KDa
SequenceString: (FME)FINRWLFST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVVVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVS SI LGAINFITTI ...String:
(FME)FINRWLFST NHKDIGTLYL LFGAWAGMVG TALSLLIRAE LGQPGTLLGD DQIYNVVVTA HAFVMIFFMV MPIMIG GFG NWLVPLMIGA PDMAFPRMNN MSFWLLPPSF LLLLASSMVE AGAGTGWTVY PPLAGNLAHA GASVDLTIFS LHLAGVS SI LGAINFITTI INMKPPAMSQ YQTPLFVWSV MITAVLLLLS LPVLAAGITM LLTDRNLNTT FFDPAGGGDP ILYQHLFW F FGHPEVYILI LPGFGMISHI VTYYSGKKEP FGYMGMVWAM MSIGFLGFIV WAHHMFTVGM DVDTRAYFTS ATMIIAIPT GVKVFSWLAT LHGGNIKWSP AMMWALGFIF LFTVGGLTGI VLANSSLDIV LHDTYYVVAH FHYVLSMGAV FAIMGGFVHW FPLFSGYTL NDTWAKIHFA IMFVGVNMTF FPQHFLGLSG MPRRYSDYPD AYTMWNTISS MGSFISLTAV MLMVFIIWEA F ASKREVLT VDLTTTNLEW LNGCPPPYHT FEEPTYVNL

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
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 26.068404 KDa
SequenceString: (FME)AYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA IILILI ALP SLRILYMMDE INNPSLTVKT MGHQWYWSYE YTDYEDLSFD SYMIPTSELK PGELRLLEVD NRVVLPMEMT IRMLVSS ED VLHSWAVPSL ...String:
(FME)AYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL THTSTMDAQE VETIWTILPA IILILI ALP SLRILYMMDE INNPSLTVKT MGHQWYWSYE YTDYEDLSFD SYMIPTSELK PGELRLLEVD NRVVLPMEMT IRMLVSS ED VLHSWAVPSL GLKTDAIPGR LNQTTLMSSR PGLYYGQCSE ICGSNHSFMP IVLELVPLKY FEKWSASML

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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 29.58718 KDa
SequenceString: QTHAYHMVNP SPWPLTGALS ALLMTSGLTM WFHFNSMTLL MIGLTTNMLT MYQWWRDVIR ESTFQGHHTP AVQKGLRYGM ILFIISEVL FFTGFFWAFY HSSLAPTPEL GGCWPPTGIH PLNPLEVPLL NTSVLLASGV SITWAHHSLM EGDRKHMLQA L FITITLGV ...String:
QTHAYHMVNP SPWPLTGALS ALLMTSGLTM WFHFNSMTLL MIGLTTNMLT MYQWWRDVIR ESTFQGHHTP AVQKGLRYGM ILFIISEVL FFTGFFWAFY HSSLAPTPEL GGCWPPTGIH PLNPLEVPLL NTSVLLASGV SITWAHHSLM EGDRKHMLQA L FITITLGV YFTLLQASEY YEAPFTISDG VYGSTFFVAT GFHGLHVIIG STFLIVCFFR QLKFHFTSNH HFGFEAAAWY WH FVDVVWL FLYVSIYWWG S

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #4: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 16.153474 KDa
SequenceString:
DYALPSYVDR RDYPLPDVAH VKNLSASQKA LKEKEKASWS SLSIDEKVEL YRLKFKESFA EMNRSTNEWK TVVGAAMFFI GFTALLLIW EKHYVYGPIP HTFEEEWVAK QTKRMLDMKV APIQGFSAKW DYDKNEWK

UniProtKB: Cytochrome c oxidase subunit 4 isoform 1, 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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 11.717269 KDa
SequenceString:
ETDEEFDARW VTYFNKPDID AWELRKGMNT LVGYDLVPEP KIIDAALRAC RRLNDFASAV RILEVVKDKA GPHKEIYPYV IQELRPTLN ELGISTPEEL GLD

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

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Macromolecule #6: Cytochrome c oxidase subunit 5B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5B, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 10.01832 KDa
SequenceString:
GGVPTDEEQA TGLEREVMLA ARKGQDPYNI LAPKATSGTK EDPNLVPSIT NKRIVGCICE EDNSTVIWFW LHKGEAQRCP SCGTHYKLV PH

UniProtKB: Cytochrome c oxidase subunit 5B, mitochondrial

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Macromolecule #7: Cytochrome c oxidase subunit 6A2, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A2, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.368521 KDa
SequenceString:
GARTWRFLTF GLALPSVALC TLNSWLHSGH RERPAFIPYH HLRIRTKPFS WGDGNHTFFH NPRVNPLPTG YE

UniProtKB: Cytochrome c oxidase subunit 6A2, mitochondrial

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Macromolecule #8: Cytochrome c oxidase subunit 6B1

MacromoleculeName: Cytochrome c oxidase subunit 6B1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.28242 KDa
SequenceString:
IKNYQTAPFD SRFPNQNQTR NCWQNYLDFH RCEKAMTAKG GDVSVCEWYR RVYKSLCPIS WVSTWDDRRA EGTFPGKI

UniProtKB: Cytochrome c oxidase subunit 6B1

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Macromolecule #9: Cytochrome c oxidase subunit 6C

MacromoleculeName: Cytochrome c oxidase subunit 6C / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.235723 KDa
SequenceString:
LAKPQMRGLL ARRLRFHIVG AFMVSLGFAT FYKFAVAEKR KKAYADFYRN YDSMKDFEEM RKAGIFQSAK

UniProtKB: Cytochrome c oxidase subunit 6C

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Macromolecule #10: Cytochrome c oxidase subunit 7A1, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7A1, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 6.189105 KDa
SequenceString:
FENRVAEKQK LFQEDNGLPV HLKGGATDNI LYRVTMTLCL GGTLYSLYCL GWASF

UniProtKB: Cytochrome c oxidase subunit 7A1, mitochondrial

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Macromolecule #11: Cytochrome c oxidase subunit 7B, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7B, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.273975 KDa
SequenceString:
DFHDKYGNAV LASGATFCVA VWVYMATQIG IEWNPSPVGR VTPKEWR

UniProtKB: Cytochrome c oxidase subunit 7B, mitochondrial

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Macromolecule #12: Cytochrome c oxidase subunit 7C, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7C, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.362319 KDa
SequenceString:
HYEEGPGKNI PFSVENKWRL LAMMTLFFGS GFAAPFFIVR HQLLKK

UniProtKB: Cytochrome c oxidase subunit 7C, mitochondrial

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Macromolecule #13: Cytochrome c oxidase subunit 8A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8A, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 4.769651 KDa
SequenceString:
IHSLPPEGKL GIMELAVGLT SCFVTFLLPA GWILSHLETY RRP

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Macromolecule #14: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 14 / Number of copies: 3 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 16 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #17: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 17 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #18: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 18 / Number of copies: 2 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Macromolecule #19: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
type: ligand / ID: 19 / Number of copies: 1 / Formula: PEK
Molecular weightTheoretical: 768.055 Da
Chemical component information

ChemComp-PEK:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / phospholipid*YM

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Macromolecule #20: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 20 / Number of copies: 1 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / 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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4161
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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