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- PDB-8yio: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azox... -

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Basic information

Entry
Database: PDB / ID: 8yio
TitleCryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state
Components
  • (Cytochrome b-c1 complex subunit ...) x 6
  • COR1 isoform 1
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • QCR6 isoform 1
KeywordsMEMBRANE PROTEIN / Complex / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


: / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / proton transmembrane transport / aerobic respiration ...: / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / cellular respiration / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / proton transmembrane transport / aerobic respiration / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / : / Cytochrome c1 / Cytochrome C1 family ...Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / : / 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 b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Chem-6PH / Chem-8PE / Chem-9PE / Chem-AZO / Chem-CN3 / Chem-CN5 / PROTOPORPHYRIN IX CONTAINING FE / Chem-UQ6 / Cytochrome b / quinol--cytochrome-c reductase ...Chem-6PH / Chem-8PE / Chem-9PE / Chem-AZO / Chem-CN3 / Chem-CN5 / PROTOPORPHYRIN IX CONTAINING FE / Chem-UQ6 / Cytochrome b / quinol--cytochrome-c reductase / : / : / : / : / : / : / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsYe, Y. / Li, Z.W. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state
Authors: Ye, Y. / Li, Z.W. / Yang, G.F.
History
DepositionFeb 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COR1 isoform 1
C: Cytochrome b
B: Cytochrome b-c1 complex subunit 2, mitochondrial
D: Cytochrome c1, heme protein, mitochondrial
N: Cytochrome b
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: QCR6 isoform 1
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9, mitochondrial
L: COR1 isoform 1
M: Cytochrome b-c1 complex subunit 2, mitochondrial
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: QCR6 isoform 1
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 9, mitochondrial
U: Cytochrome b-c1 complex subunit 10, mitochondrial
V: Cytochrome b-c1 complex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,35739
Polymers448,60420
Non-polymers11,75319
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules ALCNDOFQ

#1: Protein COR1 isoform 1 / Cytochrome b-c1 complex subunit 1 / mitochondrial


Mass: 47459.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3X1
#2: Protein Cytochrome b


Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A0G3F5W7
#4: Protein Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4


Mass: 27807.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A5B9RH60, quinol-cytochrome-c reductase
#6: Protein QCR6 isoform 1 / Cytochrome b-c1 complex subunit 6 / mitochondrial


Mass: 8983.905 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8ULB7

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Cytochrome b-c1 complex subunit ... , 6 types, 12 molecules BMEPGRHSITUV

#3: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II


Mass: 38751.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q625
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 20122.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A8H8ULJ0, quinol-cytochrome-c reductase
#7: Protein Cytochrome b-c1 complex subunit 7


Mass: 14452.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2H4
#8: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII


Mass: 10856.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PU80
#9: Protein Cytochrome b-c1 complex subunit 9, mitochondrial / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol-cytochrome c oxidoreductase subunit 9 / Ubiquinol-cytochrome c reductase 7.3 kDa protein


Mass: 6301.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The sequence of organism Saccharomyces cerevisiae is not available, replaced by P22289 temporarily.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22289
#10: Protein Cytochrome b-c1 complex subunit 10, mitochondrial / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10 ...Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10 / Ubiquinol-cytochrome c reductase 8.5 kDa protein


Mass: 5879.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The sequence of organism Saccharomyces cerevisiae is not available, replaced by P37299 temporarily.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P37299

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Non-polymers , 8 types, 19 molecules

#11: Chemical ChemComp-AZO / METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE / AZOXYSTROBIN


Mass: 403.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17N3O5 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H60O4
#13: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#14: Chemical ChemComp-9PE / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 593.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H60NO8P / Comment: phospholipid*YM
#15: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#16: Chemical ChemComp-CN5 / (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate / CARDIOLIPIN


Mass: 634.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H52O13P2
#17: Chemical ChemComp-CN3 / (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate / CARDIOLIPIN


Mass: 834.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H68O17P2
#18: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P

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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: Saccharomyces cerevisiae bc1 complex / Type: COMPLEX / Entity ID: #1, #3, #2, #4-#10 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4 / Details: PBS,0.1%DDM
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 48.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5829

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2292432
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 433970 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6YMX

6ymx


Accession code: 6YMX / Source name: PDB / Type: experimental model

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