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- PDB-29ya: Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer ... -

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Basic information

Entry
Database: PDB / ID: 29ya
TitleCryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer with one Rieske protein in the c position and one in the b position and quinone in the quinone oxidation site
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsELECTRON TRANSPORT / oxidoreductuse / proton pumping / quinol oxidation / respiration
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur 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
FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / UBIQUINONE-10 / UBIQUINONE-1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsPietras, R. / Mielecki, B. / Wojcik-Augustyn, A. / Sarewicz, M. / Jaciuk, M. / Koziej, L. / Glatt, S. / Osyczka, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2023/49/B/NZ1/02110 Poland
Ministry of Science and Higher Education (Poland)1/SOL/2021/2 Poland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Distinct ubiquinone binding at the oxidation and reduction sites of cytochrome bc.
Authors: Rafał Pietras / Anna Wójcik-Augustyn / Bohun Mielecki / Marcin Sarewicz / Marcin Jaciuk / Łukasz Koziej / Sebastian Glatt / Artur Osyczka /
Abstract: The function of cytochrome bc, a widespread energy-conserving enzyme, requires the coordinated activity of two quinone-binding sites (Q catalyzing oxidation of ubiquinol and Q catalyzing reduction of ...The function of cytochrome bc, a widespread energy-conserving enzyme, requires the coordinated activity of two quinone-binding sites (Q catalyzing oxidation of ubiquinol and Q catalyzing reduction of ubiquinone). The operation of Q, but not Q, involves large-scale movement of the head domain of iron-sulfur protein (ISP-HD). How the respective sites accommodate quinone molecules for efficient catalysis remains elusive. Here, we present high-resolution cryoelectron microscopy structures of bacterial cytochrome bc with native ubiquinone molecules in various states. They show that the quinone headgroup occupies a catalytically competent position in Q only when the ISP-HD interacts with cytochrome b. When the ISP-HD does not interact with this subunit, quinone is present in the hydrophobic groove, however its headgroup is prevented from reaching the catalytic cavity by steric hindrance. In this state, the position of quinone headgroup is clearly not fixed. In contrast, all structures show Q in the same state with a well-resolved and catalytically competent quinone headgroup, but with its tail not fixed. These distinctly different ubiquinone binding modes for Q and Q secure the smooth operation of cytochrome bc.
History
DepositionApr 14, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
B: Cytochrome b
C: Cytochrome c1
D: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,30025
Polymers197,9056
Non-polymers9,39519
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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Protein , 3 types, 6 molecules ADBECF

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 20333.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: petA, fbcF, RCAP_rcc02768 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: D5ANZ2, quinol-cytochrome-c reductase
#2: Protein Cytochrome b


Mass: 50297.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: affinity tag at C-terminus (StrepTag II)
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: petB, cytB, RCAP_rcc02769 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: D5ANZ3
#3: Protein Cytochrome c1


Mass: 28321.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: petC, RCAP_rcc02770 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: D5ANZ4

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Non-polymers , 6 types, 19 molecules

#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#6: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: native dimeric cytochrome bc1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.20 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Source (recombinant)Organism: Rhodobacter capsulatus (bacteria)
Buffer solutionpH: 8 / Details: 50mM bicine, 100mM KCl, 1mM EDTA, 0.8mM UDM
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40.22 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8883
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPU2.10.0.1941RELimage acquisition
4cryoSPARC4.7CTF correction
7UCSF ChimeraX1.1model fitting
9Coot0.9.8model refinement
10PHENIX2model refinement
11cryoSPARC4.7initial Euler assignment
13cryoSPARC4.7classification
14cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2560000 / Details: 2.56M (template) and 1.91M (TOPAZ)
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20781 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial model placement (rigid-body) into a map was done in ChimeraX
Atomic model buildingDetails: Initial model derived from a related structure determined in this study (PDB ID: XXXX)
Source name: Other / Type: experimental model
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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