8ZOS | pdb_00008zos

Cryo-EM structure of pyraclostrobin-bound porcine bc1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors.

Wang, Y.X.Ye, Y.Li, Z.W.Cui, G.R.Shi, X.X.Dong, Y.Jiang, J.J.Sun, J.Y.Guan, Z.W.Zhang, N.Wu, Q.Y.Wang, F.Zhu, X.L.Yang, G.F.

(2024) J Am Chem Soc 146: 33903-33913

  • DOI: https://doi.org/10.1021/jacs.4c12595
  • Primary Citation of Related Structures:  
    8YHQ, 8YIN, 8ZMT, 8ZOS, 8ZOW, 8ZP0

  • PubMed Abstract: 

    Cytochrome bc 1 (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (Q o I) that combats the G143A mutated isolate, which confers high resistance to strobilurin fungicides such as pyraclostrobin (PYR). The binding mode and antiresistance mechanism of MET remain unclear. Here, we determined the high-resolution structures of inhibitor-bound S. cerevisiae complex III (MET, 2.52 Å; PYR, 2.42 Å) and inhibitor-bound porcine complex III (MET, 2.53 Å; PYR, 2,37 Å) by cryo-electron microscopy. The distinct binding modes of MET and PYR were observed for the first time. Notably, the MET exhibited different binding modes in the two species. In S. cerevisiae , the binding site of MET was the same as PYR, serving as a Pm -type inhibitor of the Q o site. However, in porcine, MET acted as a dual-target inhibitor of both Q o and Q i . Based on the structural insights, a novel inhibitor (YF23694) was discovered and demonstrated excellent fungicidal activity against downy mildew and powdery mildew fungi. This work provides a new starting point for the design of the next generation of inhibitors to overcome the resistance.


  • Organizational Affiliation
    • State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bA,
L [auth a]
378Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286SF60 (Sus scrofa domesticus)
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UniProt GroupA0A286SF60
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialB,
M [auth b]
241Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AZF9 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialC,
N [auth c]
196Sus scrofaMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for F1RNZ1 (Sus scrofa)
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UniProt GroupF1RNZ1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialD,
O [auth d]
446Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0PK14 (Sus scrofa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialE,
P [auth e]
418Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RPD2 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F,
Q [auth f]
64Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7G,
R [auth g]
106Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZPR8 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8H,
S [auth h]
79Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Complex III subunit 9I,
T [auth i]
62Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10J,
U [auth j]
52Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialK,
V [auth k]
57Sus scrofaMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for A0A4X1TWD8 (Sus scrofa)
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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HA [auth a],
IA [auth a],
LA [auth g]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE
Query on PEE

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BA [auth D],
GA [auth a],
Z [auth A]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC

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AA [auth B],
JA [auth b]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DA [auth a],
EA [auth a],
X [auth A],
Y [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1D6K (Subject of Investigation/LOI)
Query on A1D6K

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CA [auth a],
W [auth A]
methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate
C19 H18 Cl N3 O4
HZRSNVGNWUDEFX-UHFFFAOYSA-N
FES
Query on FES

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FA [auth a],
KA [auth c]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection