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- EMDB-27430: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidas... -

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Basic information

Entry
Database: EMDB / ID: EMD-27430
TitleCryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs
Map data
Sample
  • Complex: Complex IVCytochrome c oxidase
    • Protein or peptide: x 9 types
  • Ligand: x 6 types
Keywordscytochrome c oxidase / Complex IV / MEMBRANE PROTEIN
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 / electron transport coupled proton transport / cytochrome-c oxidase activity / 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 / electron transport coupled proton transport / cytochrome-c oxidase activity / 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 (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsGodoy AS / Song Y / Cheruvara H / Quigley A / Oliva G
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs
Authors: Godoy AS / Song Y / Cheruvara H / Quigley A / Oliva G
History
DepositionJun 25, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27430.png

Downloads & links

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Map

FileDownload / File: emd_27430.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.829 Å
Density
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-1.6841019 - 2.9829667
Average (Standard dev.)0.003819794 (±0.07098522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27430_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_27430_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27430_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27430_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Complex IV

EntireName: Complex IVCytochrome c oxidase
Components
  • Complex: Complex IVCytochrome 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
  • Ligand: CALCIUM IONCalcium
  • Ligand: MAGNESIUM ION
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: ZINC ION

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Supramolecule #1: Complex IV

SupramoleculeName: Complex IV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 (brewer's yeast)
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

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 (brewer's 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 (brewer's yeast)
Molecular weightTheoretical: 30.383582 KDa
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

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 (brewer's yeast)
Molecular weightTheoretical: 14.188949 KDa
SequenceString:
QQKPVVKTAQ NLAEVNGPET LIGPGAKEGT VPTDLDQETG LARLELLGKL EGIDVFDTKP LDSSRKGTMK DPIIIESYDD YRYVGCTGS PAGSHTIMWL KPTVNEVARC WECGSVYKLN PVGVPNDDHH H

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 (brewer's yeast)
Molecular weightTheoretical: 14.891784 KDa
SequenceString:
AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP WAQLTEPEKQ AVWYISYGEW GPRRPVLNKG DSSFIAKGVA AGLLFSVGL FAVVRMAGGQ DAKTMNKEWQ LKSDEYLKSK NANPWGGYSQ VQSK

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 (brewer's yeast)
Molecular weightTheoretical: 12.641998 KDa
SequenceString:
SDAHDEETFE EFTARYEKEF DEAYDLFEVQ RVLNNCFSYD LVPAPAVIEK ALRAARRVND LPTAIRVFEA LKYKVENEDQ YKAYLDELK DVRQELGVPL KEELFPSSS

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 (brewer's yeast)
Molecular weightTheoretical: 6.811154 KDa
SequenceString:
ANKVIQLQKI FQSSTKPLWW RHPRSALYLY PFYAIFAVAV VTPLLYIPNA IRGIKAKKA

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 (brewer's 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 (brewer's yeast)
Molecular weightTheoretical: 6.471684 KDa
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AERKK

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

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Macromolecule #10: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #13: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 13 / 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 #14: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 14 / Number of copies: 10 / 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 #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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.011775103 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hu9

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247631
FSC plot (resolution estimation)

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