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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 3 ubiquinol oxidase.
Authors: Li, Q. / Hao, R. / Zhu, J. / Li, J.
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

Downloads & links

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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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