9UFZ | pdb_00009ufz

Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UFZ

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Literature

Structure of Acinetobacter baumannii cytochrome bo 3 ubiquinol oxidase.

Li, Q.Hao, R.Zhu, J.Li, J.

(2026) J Biological Chem 302: 111324-111324

  • DOI: https://doi.org/10.1016/j.jbc.2026.111324
  • Primary Citation Related Structures: 
    9UFB, 9UFT, 9UFV, 9UFW, 9UFZ

  • PubMed Abstract: 

    Heme-copper oxidases (heme-copper oxidoreductases) are terminal oxidases that couple oxygen reduction to proton pumping for ATP synthesis. Although our previous work has elucidated the structure and proton transfer mechanism of the Escherichia coli cytochrome bo 3 ubiquinol oxidase, the quinone dynamics and structural diversity across heme-copper oxidoreductases remain unclear. Here, we report the high-resolution cryo-EM structures of cytochrome bo 3 ubiquinol oxidase from the pathogen Acinetobacter baumannii. We captured four distinct conformational states of its native ubiquinone-8 substrate within the binding pocket. Comparative analysis revealed that conformational transitions of the substrate are directly coupled to movements of the transmembrane 0 helix. Notably, in the locked state, the substrate headgroup is stabilized by specific hydrogen bonds and adopts a distinct depth and orientation. In addition, a unique hairpin-like loop was identified in subunit II, a specific feature absent in the homologs. Our observations not only provide structural details of a pathogenic respiratory terminal oxidase but also reveal a dynamic substrate catalytic mechanism, highlighting potential avenues for targeting bacterial energy metabolism.


  • Organizational Affiliation
    • School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 146.87 kDa 
  • Atom Count: 10,264 
  • Modeled Residue Count: 1,225 
  • Deposited Residue Count: 1,225 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bo(3) ubiquinol oxidase subunit 1660Acinetobacter baumanniiMutation(s): 0 
Gene Names: APD06_18495
EC: 7.1.1.3
UniProt
Find proteins for A0AB73F7N6 (Acinetobacter baumannii)
Explore A0AB73F7N6 
Go to UniProtKB:  A0AB73F7N6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB73F7N6
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol oxidase subunit 2277Acinetobacter baumanniiMutation(s): 0 
Gene Names: cyoAABUW_1553AUO97_18960CV954_006875DWA16_13435F2P40_02915GNY86_06220
UniProt
Find proteins for A0A0D5YHQ6 (Acinetobacter baumannii)
Explore A0A0D5YHQ6 
Go to UniProtKB:  A0A0D5YHQ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D5YHQ6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bo(3) ubiquinol oxidase subunit 3191Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VBX7 (Acinetobacter baumannii)
Explore V5VBX7 
Go to UniProtKB:  V5VBX7
Entity Groups
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UniProt GroupV5VBX7
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bo(3) ubiquinol oxidase subunit 497Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VBE6 (Acinetobacter baumannii)
Explore V5VBE6 
Go to UniProtKB:  V5VBE6
Entity Groups
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UniProt GroupV5VBE6
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEO
(Subject of Investigation/LOI)

Query on HEO



Download:Ideal Coordinates CCD File
F [auth A]HEME O
C49 H58 Fe N4 O5
FRKORVCRVCLRBA-BZKSIRDQSA-L
LMG

Query on LMG



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A],
N [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
3PE
(Subject of Investigation/LOI)

Query on 3PE



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
P [auth C]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth C],
Q [auth C]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
UQ8
(Subject of Investigation/LOI)

Query on UQ8



Download:Ideal Coordinates CCD File
O [auth A]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CU
(Subject of Investigation/LOI)

Query on CU



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release