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- PDB-7deg: Cryo-EM structure of a heme-copper terminal oxidase dimer provide... -

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Basic information

Entry
Database: PDB / ID: 7deg
TitleCryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism
Components
  • (Cytochrome oxidase subunit ...) x 2
  • Cytochrome c oxidase subunit I
KeywordsOXIDOREDUCTASE / electron cryo-microscopy / heme-copper oxidase / cytochrome c oxidase dimer / Aquifex aeolicus / naphthoquinone
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 / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 ...Ba3-like heme-copper oxidase subunit I / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-DLX / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / Chem-PGV / Cytochrome oxidase subunit II / Cytochrome c oxidase subunit I
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFei, S. / Hartmut, M. / Yun, Z. / Guoliang, Z. / Shuangbo, Z.
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.0Aug 4, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 4, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 4, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 4, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 1.2Sep 17, 2025Group: Advisory / Data collection / Derived calculations
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Revision 1.2Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit I
C: Cytochrome oxidase subunit IIa
B: Cytochrome oxidase subunit II
D: Cytochrome c oxidase subunit I
F: Cytochrome oxidase subunit IIa
E: Cytochrome oxidase subunit II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,29624
Polymers172,5726
Non-polymers10,72418
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35810 Å2
ΔGint-319 kcal/mol
Surface area45120 Å2

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Cytochrome c oxidase subunit I


Mass: 65861.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (strain VF5) (bacteria) / Strain: VF5 / References: UniProt: O67937

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Cytochrome oxidase subunit ... , 2 types, 4 molecules CFBE

#2: Protein/peptide Cytochrome oxidase subunit IIa


Mass: 3944.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (bacteria)
#3: Protein Cytochrome oxidase subunit II


Mass: 16479.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (bacteria) / References: UniProt: G5DGC8

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Non-polymers , 7 types, 18 molecules

#4: Chemical ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#7: Chemical 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


Mass: 639.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H66O2
#8: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#9: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#10: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cytochrome c oxidase (respiratory complex IV) / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32982 / Symmetry type: POINT

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