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- PDB-7tlj: Rhodobacter sphaeroides Mitochondrial respiratory chain complex -

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Basic information

Entry
Database: PDB / ID: 7tlj
TitleRhodobacter sphaeroides Mitochondrial respiratory chain complex
Components
  • 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer
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 / oxidoreductase activity / electron transfer 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 Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / 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 / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / Chem-PQU / 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsXia, D. / Zhou, F. / Esser, L. / Huang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: to be published
Title: Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin
Authors: Xia, D. / Esser, L. / Zhou, F.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
H: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,17020
Polymers228,0418
Non-polymers6,12912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Cytochrome b


Mass: 50087.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q02761
#2: Protein Cytochrome c1


Mass: 29589.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cyt c1 with c-terminal hexa his tag / Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petC, fbcC / Production host: Escherichia coli (E. coli) / References: UniProt: Q02760
#3: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19928.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase
#4: Protein 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex


Mass: 14415.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost ...Details: This is the natural subunit IV. Only one helix could be determined. Subunit IV has turned out to be rather elusive in numerous crystal structures - it was never determined i.e. got lost during crystallization. Here in our CryoEM structure we see it for the first time - even though only one helix
Source: (natural) Cereibacter sphaeroides (bacteria) / References: UniProt: P16536

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Non-polymers , 5 types, 12 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-PQU / (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione


Mass: 375.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#8: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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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: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by pyramoxadone
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 250 kDa/nm / Experimental value: NO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRIS HydrochlorideTrisHCl1
20.16 %Sucrose mono caprateSMC1
30.01 %DigitoninGDN1
41 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Cytochrome bc1 complex from Rhodobacter sphaeroides with inhibitor pyramoxadone (PQ4), frozen stock 84 mg/ml. dilute to 8 mg/ml in buffer 50mM TrisHCl, pH7.5/0.16% SMC/0.01% GDN/1mM EDTA
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: 3 ul of sample blot for 3 sec. blot force 20. glow discharge for 60 sec with easy glow

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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 FIELD / Nominal magnification: 105000 X / Calibrated magnification: 60241 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 836 nm / Calibrated defocus max: 3434 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 20306 / Details: 0.05s per frame for total 50 frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 4092 / Height: 5760

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20_4444refinement
PHENIX1.20_4444refinement
EM software
IDNameVersionCategoryDetails
1cisTEM1.0.0particle selectionbeta
2SerialEM3.8.11image acquisition
4cisTEM1.0.0CTF correctionbeta
10cisTEM1.0.0initial Euler assignmentbeta
11cisTEM1.0.0final Euler assignmentbeta
12cisTEM1.0.0classificationbeta
13cisTEM1.0.03D reconstructionbeta
14SerialEM3.8.11image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5498641
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 725256 / Num. of class averages: 2 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005114732
ELECTRON MICROSCOPYf_angle_d0.684420182
ELECTRON MICROSCOPYf_chiral_restr0.04232124
ELECTRON MICROSCOPYf_plane_restr0.00632542
ELECTRON MICROSCOPYf_dihedral_angle_d17.36895080

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