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- PDB-8zom: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex -

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Basic information

Entry
Database: PDB / ID: 8zom
TitleCryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
Components
  • (Cytochrome b-c1 complex subunit ...) x 4
  • (Mitochondrial-processing peptidase subunit ...) x 2
  • Complex III subunit 9
  • Cytochrome b
  • Cytochrome c domain-containing protein
  • Ubiquinol-cytochrome c reductase complex 6.7 kDa protein
KeywordsPLANT PROTEIN / Plant complex / mitochondria / pyraclostrobin
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion ...respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Probable transposase, Ptta/En/Spm, plant / Plant transposase (Ptta/En/Spm family) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain ...Probable transposase, Ptta/En/Spm, plant / Plant transposase (Ptta/En/Spm family) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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 / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 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
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / : / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ubiquinol-cytochrome c reductase complex 6.7 kDa protein / Cytochrome b-c1 complex subunit 6 / Cytochrome c domain-containing protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / : / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ubiquinol-cytochrome c reductase complex 6.7 kDa protein / Cytochrome b-c1 complex subunit 6 / Cytochrome c domain-containing protein / Mitochondrial-processing peptidase subunit beta / Complex III subunit 9 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Mitochondrial-processing peptidase subunit alpha / Cytochrome b-c1 complex subunit 8 / Cytochrome b
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsCui, G.R. / Wang, Y.X. / 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 pyraclostrobin-bound Arachis hypogaea bc1 complex
Authors: Cui, G.R. / Wang, Y.X. / Yang, G.F.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 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

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial-processing peptidase subunit alpha
B: Mitochondrial-processing peptidase subunit beta
C: Cytochrome b
D: Cytochrome c domain-containing protein
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6
J: Complex III subunit 9
K: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein
M: Mitochondrial-processing peptidase subunit alpha
N: Mitochondrial-processing peptidase subunit beta
O: Cytochrome b
P: Cytochrome c domain-containing protein
Q: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 6
V: Complex III subunit 9
W: Ubiquinol-cytochrome c reductase complex 6.7 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)495,81651
Polymers472,30420
Non-polymers23,51231
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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Mitochondrial-processing peptidase subunit ... , 2 types, 4 molecules AMBN

#1: Protein Mitochondrial-processing peptidase subunit alpha


Mass: 49779.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445DY18
#2: Protein Mitochondrial-processing peptidase subunit beta


Mass: 54822.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445CDV5

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Protein , 3 types, 6 molecules CODPJV

#3: Protein Cytochrome b


Mass: 43360.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A8F2YUY6
#4: Protein Cytochrome c domain-containing protein / Cytochrome c1-2 / heme protein


Mass: 26894.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445B1W5
#9: Protein Complex III subunit 9 / Cytochrome b-c1 complex subunit 9


Mass: 6867.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445CQN5

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Cytochrome b-c1 complex subunit ... , 4 types, 8 molecules EQFRGSHT

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 21779.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut)
References: UniProt: A0A445CTC8, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 14022.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445CVZ9
#7: Protein Cytochrome b-c1 complex subunit 8


Mass: 8102.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A445EVJ9
#8: Protein Cytochrome b-c1 complex subunit 6


Mass: 7448.683 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A444WZ62

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Protein/peptide , 1 types, 2 molecules KW

#10: Protein/peptide Ubiquinol-cytochrome c reductase complex 6.7 kDa protein


Mass: 3073.544 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: A0A0A6ZDN8

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Non-polymers , 8 types, 31 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#13: Chemical ChemComp-A1D6K / methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate / Pyraclostrobin


Mass: 387.817 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18ClN3O4
#14: 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
#15: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#17: 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
#18: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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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: Cryo-EM structure of pyraclostrobin-bound Arachis hypogaea bc1 complex
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 500 kDa/nm / Experimental value: NO
Source (natural)Organism: Arachis hypogaea (peanut)
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 FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 49.48 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95092 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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