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- PDB-8b4o: Cryo-EM structure of cytochrome bd oxidase from C. glutamicum -

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Basic information

Entry
Database: PDB / ID: 8b4o
TitleCryo-EM structure of cytochrome bd oxidase from C. glutamicum
Components
  • Cytochrome BD ubiquinol oxidase subunit I
  • Cytochrome bd-type quinol oxidase subunit II
KeywordsOXIDOREDUCTASE / Cytochrome bd oxidase / CydAB / Membrane protein
Function / homology
Function and homology information


cytochrome complex / aerobic electron transport chain / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome ubiquinol oxidase subunit 1 / Cytochrome ubiquinol oxidase subunit 2 / Cytochrome bd terminal oxidase subunit I / Cytochrome bd terminal oxidase subunit II
Similarity search - Domain/homology
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME B/C / Cytochrome bd-type quinol oxidase subunit II / Cytochrome bd-type menaquinol oxidase subunit I
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsGrund, T.N. / Kusumoto, T. / Michel, H. / Sakamoto, J. / Safarian, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To be published
Title: Cryo-EM structure of cytochrome bd oxidase from C. glutamicum
Authors: Grund, T.N. / Michel, H. / Safarian, S.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_validate_chiral
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cytochrome bd-type quinol oxidase subunit II
A: Cytochrome BD ubiquinol oxidase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8105
Polymers92,9402
Non-polymers1,8693
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9950 Å2
ΔGint-121 kcal/mol
Surface area27260 Å2

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Components

#1: Protein Cytochrome bd-type quinol oxidase subunit II


Mass: 36261.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cydB / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cydB, CS176_1127 / Production host: Corynebacterium glutamicum (bacteria) / Strain (production host): subsp. lactofermentum / References: UniProt: A0A1Q3DPF5
#2: Protein Cytochrome BD ubiquinol oxidase subunit I / Cytochrome bd-type menaquinol oxidase subunit I


Mass: 56678.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CydA / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cydA, BBD29_06150 / Production host: Corynebacterium glutamicum (bacteria) / Strain (production host): subsp. lactofermentum / References: UniProt: Q9KWL8
#3: Chemical ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: CydAB heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.093 MDa / Experimental value: YES
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Source (recombinant)Organism: Corynebacterium glutamicum (bacteria) / Strain: subsp. lactofermentum
Buffer solutionpH: 7
SpecimenConc.: 2.5 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 R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 2100 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 107 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 995398 / Symmetry type: POINT

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