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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: PLoS One / Year: 2026
Title: Exploration of a workflow for the classification and identification of co-purified protein complexes yields new structures and multiple MSP assembly states.
Authors: Qingyang Zhang / Abhinandan Venkatesha Murthy / Carsten Mim /
Abstract: Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool ...Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool to enable structural proteomics. Additionally, image processing has evolved and can deal with conformational and compositional heterogeneity. Integrative approaches, namely mass spectrometry in conjunction with cryo-EM, have made it possible to characterize and identify complex mixtures. However, this comes at a cost of generating models and interpreting mass spectra. Here we present a modified approach that builds on publicly available software. By generating maps around 4 Å and unsupervised model building we were able to identify the most abundant proteins in our sample. This sample consisted of co-purified membrane proteins in nanodiscs. We found a novel structure and unexpected nanodisc assemblies. Our maps imply a direct interaction between membrane proteins and membrane scaffolding proteins.
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
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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