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- PDB-9ufv: Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 9ufv
TitleUbiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii
Components
  • (Cytochrome bo(3) ubiquinol oxidase subunit ...) x 3
  • Ubiquinol oxidase subunit 2
KeywordsOXIDOREDUCTASE / protein pump / ubiquinol / oxidase
Function / homology
Function and homology information


cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration ...cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome o ubiquinol oxidase, subunit I / : / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II ...Cytochrome o ubiquinol oxidase, subunit I / : / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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/quinol oxidase subunit II / 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 II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / HEME O / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Ubiquinone-8 / Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4 / Cytochrome bo(3) ubiquinol oxidase subunit 3
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsLi, J. / Zhu, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Biol Chem / Year: 2026
Title: Structure of Acinetobacter baumannii cytochrome bo ubiquinol oxidase.
Authors: Quan Li / Rui Hao / Jiapeng Zhu / Jiao Li /
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 ...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 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 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.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome bo(3) ubiquinol oxidase subunit 1
B: Ubiquinol oxidase subunit 2
C: Cytochrome bo(3) ubiquinol oxidase subunit 3
D: Cytochrome bo(3) ubiquinol oxidase subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,86917
Polymers137,7734
Non-polymers9,09613
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome bo(3) ubiquinol oxidase subunit ... , 3 types, 3 molecules ACD

#1: Protein Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome o ubiquinol oxidase subunit 1 / Oxidase bo(3) subunit 1 / Ubiquinol oxidase polypeptide ...Cytochrome o ubiquinol oxidase subunit 1 / Oxidase bo(3) subunit 1 / Ubiquinol oxidase polypeptide I / Ubiquinol oxidase subunit 1


Mass: 74200.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: APD06_18495 / Production host: Escherichia coli (E. coli)
References: UniProt: A0AB73F7N6, ubiquinol oxidase (H+-transporting)
#3: Protein Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome o ubiquinol oxidase subunit 3 / Oxidase bo(3) subunit 3 / Ubiquinol oxidase polypeptide ...Cytochrome o ubiquinol oxidase subunit 3 / Oxidase bo(3) subunit 3 / Ubiquinol oxidase polypeptide III / Ubiquinol oxidase subunit 3


Mass: 21569.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: cyoC, A7M90_03870, ABR2091_2328, ABUW_1551, APD33_01250, AUO97_18970, B9W25_06685, B9X95_00860, CBE85_07950, CPI82_06240, CV954_006865, DOL94_04060, DWA16_13445, EA686_23140, EA706_07065, EA722_ ...Gene: cyoC, A7M90_03870, ABR2091_2328, ABUW_1551, APD33_01250, AUO97_18970, B9W25_06685, B9X95_00860, CBE85_07950, CPI82_06240, CV954_006865, DOL94_04060, DWA16_13445, EA686_23140, EA706_07065, EA722_12355, EJ062_16285, F2P40_02905, F4T83_12045, FJU42_07370, FPK81_02680, FQZ18_07140, G3N53_06175, GNY86_06230, GSE42_12855, IAG11_14320, IHV20_11645, IMO23_11635, J6E47_07065, JHZ39_000762, LV35_04001, MKP18_000452, P9867_011725, P9867_07390, SAMEA104305318_03259, SAMEA104305343_01084, SAMEA4394745_02479
Production host: Escherichia coli (E. coli) / References: UniProt: V5VBX7
#4: Protein Cytochrome bo(3) ubiquinol oxidase subunit 4 / Cytochrome o ubiquinol oxidase subunit 4 / Oxidase bo(3) subunit 4 / Ubiquinol oxidase polypeptide ...Cytochrome o ubiquinol oxidase subunit 4 / Oxidase bo(3) subunit 4 / Ubiquinol oxidase polypeptide IV / Ubiquinol oxidase subunit 4


Mass: 10882.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: cyoD, A7M90_03875, ABR2091_2329, ABUW_1550, APD33_01245, AUO97_18975, B9W25_06690, B9X95_00865, C5U34_10105, CBE85_07945, CPI82_06245, CV954_006860, DOL94_04065, DWA16_13450, EA706_07070, EA722_ ...Gene: cyoD, A7M90_03875, ABR2091_2329, ABUW_1550, APD33_01245, AUO97_18975, B9W25_06690, B9X95_00865, C5U34_10105, CBE85_07945, CPI82_06245, CV954_006860, DOL94_04065, DWA16_13450, EA706_07070, EA722_12360, EJ062_16280, F2P40_02900, F4T83_12050, FJU42_07375, FPK81_02675, FQZ18_07135, G3N53_06180, GNY86_06235, GSE42_12860, IAG11_14315, IHV20_11650, IMO23_11640, J6E47_07060, JHZ39_000761, LV35_04000, MKP18_000451, P9867_011730, P9867_07395, SAMEA104305318_03260, SAMEA104305343_01083, SAMEA4394745_02480
Production host: Escherichia coli (E. coli) / References: UniProt: V5VBE6

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Protein , 1 types, 1 molecules B

#2: Protein Ubiquinol oxidase subunit 2


Mass: 31121.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: cyoA, ABUW_1553, AUO97_18960, CV954_006875, DWA16_13435, F2P40_02915, GNY86_06220
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5YHQ6

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Non-polymers , 6 types, 13 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HEO / HEME O


Mass: 838.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H58FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#8: 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.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#9: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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 bo(3) ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46373 / Symmetry type: POINT
RefinementHighest resolution: 3.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01310602
ELECTRON MICROSCOPYf_angle_d1.40914386
ELECTRON MICROSCOPYf_dihedral_angle_d10.3681669
ELECTRON MICROSCOPYf_chiral_restr0.081570
ELECTRON MICROSCOPYf_plane_restr0.0081709

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