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- EMDB-14436: Monomeric respiratory complex IV isolated from S. cerevisiae -

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Basic information

Entry
Database: EMDB / ID: EMD-14436
TitleMonomeric respiratory complex IV isolated from S. cerevisiae
Map dataMonomeric mitochondrial complex IV (cytochrome c oxidase) isolated from S. cerevisiae.
Sample
  • Complex: Cytochrome c oxidase
    • Complex: Cytochrome c oxidase
      • Protein or peptide: x 9 types
  • Ligand: x 6 types
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / proton transmembrane transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / 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 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 VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / 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 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / 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 I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / 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 oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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. / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsMarechal A / Hartley A / Ing G / Pinotsis N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M00936X/1 United Kingdom
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2022
Title: Cryo-EM structure of a monomeric yeast S. cerevisiae complex IV isolated with maltosides: Implications in supercomplex formation.
Authors: Gabriel Ing / Andrew M Hartley / Nikos Pinotsis / Amandine Maréchal /
Abstract: In mitochondria, complex IV (CIV) can be found as a monomer, a dimer or in association with other respiratory complexes. The atomic structure of the yeast S. cerevisiae CIV in a supercomplex (SC) ...In mitochondria, complex IV (CIV) can be found as a monomer, a dimer or in association with other respiratory complexes. The atomic structure of the yeast S. cerevisiae CIV in a supercomplex (SC) with complex III (CIII) pointed to a region of significant conformational changes compared to the homologous mammalian CIV structures. These changes involved the matrix side domain of Cox5A at the CIII-CIV interface, and it was suggested that it could be required for SC formation. To investigate this, we solved the structure of the isolated monomeric CIV from S. cerevisiae stabilised in amphipol A8-35 at 3.9 Å using cryo-electron microscopy. Only a minor change in flexibility was seen in this Cox5A region, ruling out large CIV conformational shift for interaction with CIII and confirming the different fold of the yeast Cox5A subunit compared to mammalian homologues. Other differences in structure were the absence of two canonical subunits, Cox12 and Cox13, as well as Cox26, which is unique to the yeast CIV. Their absence is most likely due to the protein purification protocol used to isolate CIV from the III-IV SC.
History
DepositionFeb 24, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14436.png

Downloads & links

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Map

FileDownload / File: emd_14436.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomeric mitochondrial complex IV (cytochrome c oxidase) isolated from S. cerevisiae.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 256 pix.
= 208.64 Å		0.82 Å/pix.
x 256 pix.
= 208.64 Å		0.82 Å/pix.
x 256 pix.
= 208.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.815 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6
Minimum - Maximum-14.394205 - 23.829657
Average (Standard dev.)2.3226737e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 208.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cytochrome c oxidase

EntireName: Cytochrome c oxidase
Components
  • Complex: Cytochrome c oxidase
    • 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; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3
      • Protein or peptide: Cytochrome c oxidase subunit 4, mitochondrial
      • Protein or peptide: Cytochrome c oxidase polypeptide 5A, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7
      • Protein or peptide: Cytochrome c oxidase polypeptide VIII, mitochondrial
      • Protein or peptide: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: MAGNESIUM ION
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION

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Supramolecule #1: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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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 S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.832586 KDa
SequenceString: MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT ...String:
MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT TLNMRTNGMT MHKLPLFVWS IFITAFLLLL SLPVLSAGIT MLLLDRNFNT SFFEVSGGGD PILYEHLFWF FG HPEVYIL IIPGFGIISH VVSTYSKKPV FGEISMVYAM ASIGLLGFLV WSHHMYIVGL DADTRAYFTS ATMIIAIPTG IKI FSWLAT IHGGSIRLAT PMLYAIAFLF LFTMGGLTGV ALANASLDVA FHDTYYVVGH FHYVLSMGAI FSLFAGYYYW SPQI LGLNY NEKLAQIQFW LIFIGANVIF FPMHFLGING MPRRIPDYPD AFAGWNYVAS IGSFIATLSL FLFIYILYDQ LVNGL NNKV NNKSVIYNKA PDFVESNTIF NLNTVKSSSI EFLLTSPPAV HSFNTPAVQS

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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 S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.779816 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #3: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 30.383582 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL ...String:
MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL SGLLITFWLI VIFVTCQYIE YTNAAFTISD GVYGSVFYAG TGLHFLHMVM LAAMLGVNYW RMRNYHLTAG HH VGYETTI IYTHVLDVIW LFLYVVFYWW GV

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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 S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.044794 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
PVVKTAQNLA EVNGPETLIG PGAKEGTVPT DLDQETGLAR LELLGKLEGI DVFDTKPLDS SRKGTMKDPI IIESYDDYRY VGCTGSPAG SHTIMWLKPT VNEVARCWEC GSVYKLNPVG VP

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

MacromoleculeName: Cytochrome c oxidase polypeptide 5A, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.891784 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP WAQLTEPEKQ AVWYISYGEW GPRRPVLNKG DSSFIAKGVA AGLLFSVGL FAVVRMAGGQ DAKTMNKEWQ LKSDEYLKSK NANPWGGYSQ VQSK

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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 S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 12.230607 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
DEETFEEFTA RYEKEFDEAY DLFEVQRVLN NCFSYDLVPA PAVIEKALRA ARRVNDLPTA IRVFEALKYK VENEDQYKAY LDELKDVRQ ELGVPLKEEL FPSSS

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Macromolecule #7: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POL...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 6.811154 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
ANKVIQLQKI FQSSTKPLWW RHPRSALYLY PFYAIFAVAV VTPLLYIPNA IRGIKAKKA

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Macromolecule #8: Cytochrome c oxidase polypeptide VIII, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide VIII, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 5.375354 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
VHFKDGVYEN IPFKVKGRKT PYALSHFGFF AIGFAVPFVA CYVQLKK

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Macromolecule #9: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE PO...

MacromoleculeName: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 6.471684 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AERKK

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Macromolecule #10: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #11: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 11 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 13 / Number of copies: 3 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #14: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / 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: 7.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters of sample applied to negatively glow discharged grig..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 558378
Details: Manual picking of 970 particles followed 2D classification, selection of best classes (271 particles) and autopicking by CryoSPARC template picker.
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10) / Software - details: Run through cryoSPARC wrapper
Startup modelType of model: NONE / Details: Model was generated ab initio in cryosparc
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4) / Details: Cryosparc ab-initio model reconstruction
Final 3D classificationNumber classes: 30 / Avg.num./class: 2413 / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4) / Details: Cyosparc 3D refinement
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Details: CyroSPARC non-uniform refinement was performed / Number images used: 72409
FSC plot (resolution estimation)

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