7DEG | pdb_00007deg

Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors.

Zhu, G.Zeng, H.Zhang, S.Juli, J.Tai, L.Zhang, D.Pang, X.Zhang, Y.Lam, S.M.Zhu, Y.Peng, G.Michel, H.Sun, F.

(2021) Angew Chem Int Ed Engl 60: 13323-13330

  • DOI: https://doi.org/10.1002/anie.202016785
  • Primary Citation Related Structures: 
    7DEG

  • PubMed 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 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.


  • Organizational Affiliation
    • National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.

Macromolecule Content 

  • Total Structure Weight: 183.3 kDa 
  • Atom Count: 12,852 
  • Modeled Residue Count: 1,520 
  • Deposited Residue Count: 1,532 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit I
A, D
587Aquifex aeolicus VF5Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O67937 (Aquifex aeolicus (strain VF5))
Explore O67937 
Go to UniProtKB:  O67937
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67937
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome oxidase subunit IIaB [auth C],
E [auth F]
32Aquifex aeolicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for G0LWX8 (Aquifex aeolicus)
Explore G0LWX8 
Go to UniProtKB:  G0LWX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0LWX8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome oxidase subunit IIC [auth B],
F [auth E]
147Aquifex aeolicusMutation(s): 0 
UniProt
Find proteins for G5DGC8 (Aquifex aeolicus)
Explore G5DGC8 
Go to UniProtKB:  G5DGC8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5DGC8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HAS

Query on HAS



Download:Ideal Coordinates CCD File
G [auth A],
Q [auth D]
HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-ZOMLSHGTSA-L
PGV

Query on PGV



Download:Ideal Coordinates CCD File
K [auth A]
M [auth A]
N [auth C]
P [auth D]
U [auth D]
K [auth A],
M [auth A],
N [auth C],
P [auth D],
U [auth D],
W [auth F]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
L [auth A],
V [auth D]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
DLX

Query on DLX



Download:Ideal Coordinates CCD File
J [auth A],
T [auth D]
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
C45 H66 O2
HQTZEMLTZXAZEE-ZTUUOAHYSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
H [auth A],
R [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CUA

Query on CUA



Download:Ideal Coordinates CCD File
O [auth B],
X [auth E]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
I [auth A],
S [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations