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- EMDB-30657: Cryo-EM structure of a heme-copper terminal oxidase dimer provide... -

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Basic information

Entry
Database: EMDB / ID: EMD-30657
TitleCryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism
Map data
Sample
  • Complex: cytochrome c oxidase (respiratory complex IV)
    • Protein or peptide: Cytochrome c oxidase subunit I
    • Protein or peptide: Cytochrome oxidase subunit IIa
    • Protein or peptide: Cytochrome oxidase subunit II
  • Ligand: HEME-AS
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: COPPER (II) ION
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: DINUCLEAR COPPER ION
Keywordselectron cryo-microscopy / heme-copper oxidase / cytochrome c oxidase dimer / Aquifex aeolicus / naphthoquinone / OXIDOREDUCTASE
Function / homology
Function and homology information


cell envelope / cytochrome-c oxidase activity / aerobic respiration / copper ion binding / heme binding / membrane
Similarity search - Function
Ba3-like heme-copper oxidase subunit I / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 ...Ba3-like heme-copper oxidase subunit I / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 oxidase subunit II / Cytochrome c oxidase subunit I
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria) / Aquifex aeolicus (strain VF5) (bacteria) / Aquifex aeolicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFei S / Hartmut M
CitationJournal: Angew Chem Int Ed Engl / Year: 2021
Title: The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors.
Authors: Guoliang Zhu / Hui Zeng / Shuangbo Zhang / Jana Juli / Linhua Tai / Danyang Zhang / Xiaoyun Pang / Yan Zhang / Sin Man Lam / Yun Zhu / Guohong Peng / Hartmut Michel / Fei Sun /
Abstract: The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family ...The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.
History
DepositionNov 4, 2020-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7deg
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30657.png

Downloads & links

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Map

FileDownload / File: emd_30657.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.051110007 - 0.07655099
Average (Standard dev.)0.0001745497 (±0.002083544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0510.0770.000

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Supplemental data

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Sample components

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Entire : cytochrome c oxidase (respiratory complex IV)

EntireName: cytochrome c oxidase (respiratory complex IV)
Components
  • Complex: cytochrome c oxidase (respiratory complex IV)
    • Protein or peptide: Cytochrome c oxidase subunit I
    • Protein or peptide: Cytochrome oxidase subunit IIa
    • Protein or peptide: Cytochrome oxidase subunit II
  • Ligand: HEME-AS
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: COPPER (II) ION
  • Ligand: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: DINUCLEAR COPPER ION

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Supramolecule #1: cytochrome c oxidase (respiratory complex IV)

SupramoleculeName: cytochrome c oxidase (respiratory complex IV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)

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Macromolecule #1: Cytochrome c oxidase subunit I

MacromoleculeName: Cytochrome c oxidase subunit I / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5
Molecular weightTheoretical: 65.861594 KDa
SequenceString: VSNAIKFIIL TEIIFPTLLL VFGIYHGVMQ VFYRSGIIKA ESFLGIDYYQ GLTLHGVINV IVYTTIFIVG FSNAIVAYSL KKPLREKVQ WIALGMMVIG TLMAAWAMFT GRATVLYTFY PPLIAHWTFY LGAVLLVLGS LVPFFFDWIP SAIQWKRENP D QKLPLAVF ...String:
VSNAIKFIIL TEIIFPTLLL VFGIYHGVMQ VFYRSGIIKA ESFLGIDYYQ GLTLHGVINV IVYTTIFIVG FSNAIVAYSL KKPLREKVQ WIALGMMVIG TLMAAWAMFT GRATVLYTFY PPLIAHWTFY LGAVLLVLGS LVPFFFDWIP SAIQWKRENP D QKLPLAVF GTFVNFILWT IMIVPVAIEI LFQLLPLSLG LVDEINPLLA RTLFWFFGHP VVYFWLLPAY VALYTILPKI VS EKGKLYS DPAARLAFIL FLIFSLPVGL HHQFTDPGIT NTWKLIHALF TFGVALPSMI TAFTVATSLE YSVKAEHPEL KNS KFYWWT FLPFMRLEGN KWMFSYFFAG LVLFFIGGIT GIVNASYNVN LVVHNTAYVP GHFHTTVGGL VLLVFFALSL YMVS KLRGS EVKLKGLAVL APYFWMQGMF MFSYAMMVGG VVVGFPRRTN AGLTYLNPDS PLYRPEWTGY AQLAAVGGVL LAIGF AFYF ASLIATALAP KVRESTLEFP IADAYHDAPA PLLNNLKTWT VAAIILAVLS YIPPLYDASV RGVFFKSPAY NEKFPM PLK QLQGAEKKEE KKELSKAEGG ITQK

UniProtKB: Cytochrome c oxidase subunit I

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Macromolecule #2: Cytochrome oxidase subunit IIa

MacromoleculeName: Cytochrome oxidase subunit IIa / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 3.944789 KDa
SequenceString:
FFPSGTIAFF IFMMVFYAVL WFMIYWVLLE RG

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Macromolecule #3: Cytochrome oxidase subunit II

MacromoleculeName: Cytochrome oxidase subunit II / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 16.479371 KDa
SequenceString:
RAEKTGLTLA LILLLTFFSL IVYAAKGLKI DIPTCVTDVE PFQEGKLIKH GDKRYELHIL ARMWYFDFNK GATEIKIPVG SVVDIFTTS KDVVHGVHIH GTNYNVMAIP GTVGYMRIKF EKPGVYHVVC HEFCGVGHHA MQGKIIVE

UniProtKB: Cytochrome oxidase subunit II

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Macromolecule #4: HEME-AS

MacromoleculeName: HEME-AS / type: ligand / ID: 4 / Number of copies: 2 / Formula: HAS
Molecular weightTheoretical: 920.954 Da
Chemical component information

ChemComp-HAS:
HEME-AS

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #6: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #7: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-h...

MacromoleculeName: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
type: ligand / ID: 7 / Number of copies: 2 / Formula: DLX
Molecular weightTheoretical: 639.004 Da
Chemical component information

ChemComp-DLX:
2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione

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Macromolecule #8: (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: 8 / Number of copies: 6 / 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 #9: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 9 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #10: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32982
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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