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- PDB-9hwk: Structure of the Cytochrome o ubiquinol oxidase embedded in the n... -

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Basic information

Entry
Database: PDB / ID: 9hwk
TitleStructure of the Cytochrome o ubiquinol oxidase embedded in the nanodisc
Components(Cytochrome bo(3) ubiquinol oxidase subunit ...) x 4
KeywordsELECTRON TRANSPORT / 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 III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / 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 III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / 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 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / HEME O / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsMim, C. / Zhang, Q. / Murthy, A.V.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 21:1630 Sweden
CitationJournal: To Be Published
Title: In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states
Authors: Zhang, Q. / Murthy, A.V. / Mim, C.
History
DepositionJan 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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
F: Cytochrome bo(3) ubiquinol oxidase subunit 1
G: Cytochrome bo(3) ubiquinol oxidase subunit 2
H: Cytochrome bo(3) ubiquinol oxidase subunit 3
I: Cytochrome bo(3) ubiquinol oxidase subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6368
Polymers144,0524
Non-polymers1,5844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytochrome bo(3) ubiquinol oxidase subunit ... , 4 types, 4 molecules FGHI

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


Mass: 74424.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0ABJ0, ubiquinol oxidase (H+-transporting)
#2: Protein Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome o ubiquinol oxidase subunit 2 / Cytochrome o subunit 2 / Oxidase bo(3) subunit 2 / ...Cytochrome o ubiquinol oxidase subunit 2 / Cytochrome o subunit 2 / Oxidase bo(3) subunit 2 / Ubiquinol oxidase chain B / Ubiquinol oxidase polypeptide II / Ubiquinol oxidase subunit 2


Mass: 34947.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABJ2
#3: Protein Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome o ubiquinol oxidase subunit 3 / Cytochrome o subunit 3 / Oxidase bo(3) subunit 3 / ...Cytochrome o ubiquinol oxidase subunit 3 / Cytochrome o subunit 3 / Oxidase bo(3) subunit 3 / Ubiquinol oxidase chain C / Ubiquinol oxidase polypeptide III / Ubiquinol oxidase subunit 3


Mass: 22642.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABJ4
#4: Protein Cytochrome bo(3) ubiquinol oxidase subunit 4 / Cytochrome o ubiquinol oxidase subunit 4 / Cytochrome o subunit 4 / Oxidase bo(3) subunit 4 / ...Cytochrome o ubiquinol oxidase subunit 4 / Cytochrome o subunit 4 / Oxidase bo(3) subunit 4 / Ubiquinol oxidase chain D / Ubiquinol oxidase polypeptide IV / Ubiquinol oxidase subunit 4


Mass: 12037.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABJ7

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Non-polymers , 4 types, 4 molecules

#5: Chemical ChemComp-HEO / HEME O


Mass: 838.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H58FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / 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: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 50mM HEPES, 150mM NaCl and 5mM EGTA
SpecimenConc.: 4.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 100% humidity, 16C

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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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7ISOLDEmodel fitting
9cryoSPARCinitial Euler assignment
12cryoSPARC3D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 794072
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160179 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Atomic model buildingPDB-ID: 2hrt

2hrt


Accession code: 2hrt / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0092403716199020.0118210261
ELECTRON MICROSCOPYs_angle_nonh_d1.9929957135061.7828417

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