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- PDB-8smr: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8smr
Titlecytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Components
  • Cbb3-type Cytochrome C oxidase subunit II
  • Cbb3-type cytochrome c oxidase subunit
  • Cytochrome C5
  • Cytochrome b
  • Cytochrome c1
  • Cytochrome c4
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
  • cytochrome-c oxidaseCytochrome c oxidase
KeywordsMEMBRANE PROTEIN / Electron transport chain / Supercomplex / Pseudomonas aeruginosa
Function / homology
Function and homology information


cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain ...cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome c4-like / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c, class IE / Cytochrome c, class IC ...Cytochrome c4-like / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c, class IE / Cytochrome c, class IC / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome b / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-I7Y / UBIQUINONE-10 / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cbb3-type cytochrome c oxidase subunit / Cytochrome b/c1 / C-type cytochrome ...COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-I7Y / UBIQUINONE-10 / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cbb3-type cytochrome c oxidase subunit / Cytochrome b/c1 / C-type cytochrome / Cbb3-type cytochrome c oxidase subunit II / cytochrome-c oxidase / Cytochrome b / Cytochrome C5
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDi Trani, J.M. / Rubinstein, J.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of the - respiratory supercomplex from .
Authors: Justin M Di Trani / Andreea A Gheorghita / Madison Turner / Peter Brzezinski / Pia Ädelroth / Siavash Vahidi / P Lynne Howell / John L Rubinstein /
Abstract: Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that ...Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that enables ATP synthesis and membrane transport. These protein complexes can also form higher order assemblies known as respiratory supercomplexes (SCs). The electron transport chain of the opportunistic pathogen is closely linked with its ability to invade host tissue, tolerate harsh conditions, and resist antibiotics but is poorly characterized. Here, we determine the structure of a SC that forms between the quinol:cytochrome oxidoreductase (cytochrome ) and one of the organism's terminal oxidases, cytochrome , which is found only in some bacteria. Remarkably, the SC structure also includes two intermediate electron carriers: a diheme cytochrome and a single heme cytochrome . Together, these proteins allow electron transfer from ubiquinol in cytochrome to oxygen in cytochrome . We also present evidence that different isoforms of cytochrome can participate in formation of this SC without changing the overall SC architecture. Incorporating these different subunit isoforms into the SC would allow the bacterium to adapt to different environmental conditions. Bioinformatic analysis focusing on structural motifs in the SC suggests that cytochrome - SCs also exist in other bacterial pathogens.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
I: Cytochrome b
J: Cytochrome c1
K: Cytochrome c4
L: Cytochrome C5
Z: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
M: Cytochrome c1
N: Cytochrome c4
O: Cytochrome C5
E: cytochrome-c oxidase
F: Cbb3-type Cytochrome C oxidase subunit II
G: Cbb3-type cytochrome c oxidase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,52937
Polymers359,33213
Non-polymers13,19824
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 13 molecules CZIDJMKNLOEFG

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 20561.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069Q0N5
#2: Protein Cytochrome b /


Mass: 46111.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071LG61
#3: Protein Cytochrome c1 /


Mass: 26280.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069Q767
#4: Protein Cytochrome c4


Mass: 18696.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071L1H9
#5: Protein Cytochrome C5


Mass: 13475.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A211VLT6
#6: Protein cytochrome-c oxidase / Cytochrome c oxidase


Mass: 52586.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071LDU2
#7: Protein Cbb3-type Cytochrome C oxidase subunit II


Mass: 22417.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071L2F4
#8: Protein Cbb3-type cytochrome c oxidase subunit


Mass: 34078.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069Q0W4

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Non-polymers , 7 types, 24 molecules

#9: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#12: Chemical ChemComp-I7Y / (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 855.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H74O15
#13: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#14: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#15: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN

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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 bc1-cbb3 supercomplex / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightValue: 374 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48594 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324943
ELECTRON MICROSCOPYf_angle_d0.6834152
ELECTRON MICROSCOPYf_dihedral_angle_d10.9323454
ELECTRON MICROSCOPYf_chiral_restr0.043589
ELECTRON MICROSCOPYf_plane_restr0.0044245

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