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- EMDB-57440: Cytochrome bc1 complex from Rhodobacter capsulatus at 2.16 A reso... -

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Basic information

Entry
Database: EMDB / ID: EMD-57440
TitleCytochrome bc1 complex from Rhodobacter capsulatus at 2.16 A resolution
Map dataWT cons main map
Sample
  • Complex: native dimeric cytochrome bc1 complex
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: UNDECYL-MALTOSIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-1
  • Ligand: HEME C
  • Ligand: water
Keywordsoxidoreductuse / proton pumping / quinol oxidation / respiration / ELECTRON TRANSPORT
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
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsPietras R / Mielecki B / Wojcik-Augustyn A / Sarewicz M / Jaciuk M / Koziej L / Glatt S / Osyczka A
Funding support Poland, 2 items
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, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57440.png

Downloads & links

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Map

FileDownload / File: emd_57440.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWT cons main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 304.416 Å		0.85 Å/pix.
x 360 pix.
= 304.416 Å		0.85 Å/pix.
x 360 pix.
= 304.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8456 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.10737824 - 0.3334837
Average (Standard dev.)0.00044572185 (±0.0068468098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 304.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57440_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: WT cons sharpened map

Fileemd_57440_additional_1.map
AnnotationWT cons sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: WT cons half map B

Fileemd_57440_half_map_1.map
AnnotationWT cons half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: WT cons half map A

Fileemd_57440_half_map_2.map
AnnotationWT cons half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : native dimeric cytochrome bc1 complex

EntireName: native dimeric cytochrome bc1 complex
Components
  • Complex: native dimeric cytochrome bc1 complex
    • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: UNDECYL-MALTOSIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-1
  • Ligand: HEME C
  • Ligand: water

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Supramolecule #1: native dimeric cytochrome bc1 complex

SupramoleculeName: native dimeric cytochrome bc1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 200 KDa

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

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 20.333914 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString:
SHAEDNAGTR RDFLYHATAA TGVVVTGAAV WPLINQMNAS ADVKAMASIF VDVSAVEVGT QLTVKWRGKP VFIRRRDEKD IELARSVPL GALRDTSAEN ANKPGAEATD ENRTLPAFDG TNTGEWLVML GVCTHLGCVP MGDKSGDFGG WFCPCHGSHY D SAGRIRKG PAPRNLDIPV AAFVDETTIK LG

UniProtKB: Ubiquinol-cytochrome c reductase iron-sulfur subunit

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Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Details: affinity tag at C-terminus (StrepTag II) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 50.297418 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: SGIPHDHYEP KTGIEKWLHD RLPIVGLVYD TIMIPTPKNL NWWWIWGIVL AFTLVLQIVT GIVLAMHYTP HVDLAFASVE HIMRDVNGG WAMRYIHANG ASLFFLAVYI HIFRGLYYGS YKAPREITWI VGMVIYLLMM GTAFMGYVLP WGQMSFWGAT V ITGLFGAI ...String:
SGIPHDHYEP KTGIEKWLHD RLPIVGLVYD TIMIPTPKNL NWWWIWGIVL AFTLVLQIVT GIVLAMHYTP HVDLAFASVE HIMRDVNGG WAMRYIHANG ASLFFLAVYI HIFRGLYYGS YKAPREITWI VGMVIYLLMM GTAFMGYVLP WGQMSFWGAT V ITGLFGAI PGIGPSIQAW LLGGPAVDNA TLNRFFSLHY LLPFVIAALV AIHIWAFHTT GNNNPTGVEV RRTSKADAEK DT LPFWPYF VIKDLFALAL VLLGFFAVVA YMPNYLGHPD NYVQANPLST PAHIVPEWYF LPFYAILRAF AADVWVVILV DGL TFGIVD AKFFGVIAMF GAIAVMALAP WLDTSKVRSG AYRPKFRMWF WFLVLDFVVL TWVGAMPTEY PYDWISLIAS TYWF AYFLV ILPLLGATEK PEPIPASIEE DFNSHYGNPA EWSHPQFEK

UniProtKB: Cytochrome b

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Macromolecule #3: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 28.321121 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: NSNVPDHAFS FEGIFGKYDQ AQLRRGFQVY NEVCSACHGM KFVPIRTLAD DGGPQLDPTF VREYAAGLDT IIDKDSGEER DRKETDMFP TRVGDGMGPD LSVMAKARAG FSGPAGSGMN QLFKGMGGPE YIYNYVIGFE ENPECAPEGI DGYYYNKTFQ I GGVPDTCK ...String:
NSNVPDHAFS FEGIFGKYDQ AQLRRGFQVY NEVCSACHGM KFVPIRTLAD DGGPQLDPTF VREYAAGLDT IIDKDSGEER DRKETDMFP TRVGDGMGPD LSVMAKARAG FSGPAGSGMN QLFKGMGGPE YIYNYVIGFE ENPECAPEGI DGYYYNKTFQ I GGVPDTCK DAAGVKITHG SWARMPPPLV DDQVTYEDGT PATVDQMAQD VSAFLMWAAE PKLVARKQMG LVAMVMLGLL SV MLYLTNK RLWAPYKGHK A

UniProtKB: Cytochrome c1

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Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #5: UNDECYL-MALTOSIDE

MacromoleculeName: UNDECYL-MALTOSIDE / type: ligand / ID: 5 / Number of copies: 8 / Formula: UMQ
Molecular weightTheoretical: 496.589 Da
Chemical component information

ChemComp-UMQ:
UNDECYL-MALTOSIDE / detergent*YM

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Macromolecule #6: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 6 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #7: UBIQUINONE-1

MacromoleculeName: UBIQUINONE-1 / type: ligand / ID: 7 / Number of copies: 2 / Formula: UQ1
Molecular weightTheoretical: 250.29 Da
Chemical component information

ChemComp-UQ1:
UBIQUINONE-1

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Macromolecule #8: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 620.519 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 177 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 8 / Details: 50mM bicine, 100mM KCl, 1mM EDTA, 0.8mM UDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8883 / Average electron dose: 40.22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2560000 / Details: 2.56M (template) and 1.91M (TOPAZ)
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 169557
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7)
Details: Ab initio reconstruction into three classes followed by heterogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1zrt


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial model placement (rigid-body) into a map was done in ChimeraX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-29xz:
Cryo-EM structure of Rhodobacter capsulatus cytochrome bc1 dimer at 2.16 A resolution with water molecules and quinone in the quinone reduction site

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