SMTL ID : 8yhq.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in pyraclostrobin-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-mer

Ligands

2 x 6PH: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate(Non-covalent)

6PH.1: 10 residues within 4Å: Chain A: M.429 Chain B: I.17, S.34, H.222, I.226, D.229, L.230 Chain E: V.30 Ligands: UQ6.7, 7PH.10 12 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:I.17, B:I.226, B:I.226, B:D.229, B:L.230, B:L.230, E:V.30 Hydrogen bonds: B:S.223, A:S.424, A:S.424 Salt bridges: B:H.222, B:H.222 6PH.18: 13 residues within 4Å: Chain G: I.17, S.34, I.226, D.229, L.230, F.234 Chain K: M.429 Chain N: V.30, M.33, S.37 Chain R: F.14 Ligands: CN5.6, UQ6.11 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain R Hydrophobic interactions: G:I.17, G:I.226, G:D.229, G:L.230, G:F.234 Hydrogen bonds: R:N.11

2 x 9PE: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(Non-covalent)

9PE.2: 8 residues within 4Å: Chain B: F.3, S.6, N.7 Chain G: T.112, N.115, M.196, M.199 Ligands: CN5.6 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:T.112, G:N.115, B:S.6, B:N.7 9PE.12: 10 residues within 4Å: Chain B: T.112, N.115, A.192, I.195, M.196 Chain G: F.3, S.6, N.7, V.8 Ligands: CN5.6 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain B Hydrogen bonds: G:S.6, G:N.7, G:V.8, B:N.115 Hydrophobic interactions: B:N.115, B:I.195

6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 15 residues within 4Å: Chain B: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, T.127, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.40, B:Q.43, B:I.48, B:T.127, B:V.135, B:Y.184, B:Y.184 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.82, B:H.183 HEM.4: 18 residues within 4Å: Chain B: W.30, G.33, L.36, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, V.194, H.197, L.201, S.206, S.207 Ligands: UQ6.7 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:L.36, B:L.36, B:L.113, B:W.114, B:I.120, B:V.194, B:L.201 Hydrogen bonds: B:G.33, B:S.105, B:S.206, B:S.207 Salt bridges: B:H.96, B:K.99, B:K.99, B:R.110 Metal complexes: B:H.96, B:H.197 HEM.9: 18 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, P.113, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168, V.190 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:V.39, D:P.113, D:I.130, D:L.134, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167, D:V.167, D:L.168, D:V.190 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.13: 16 residues within 4Å: Chain G: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:L.40, G:Q.43, G:I.48, G:T.127, G:V.135, G:F.180, G:Y.184, G:Y.184 Salt bridges: G:R.79, G:R.79 Metal complexes: G:H.82, G:H.183 HEM.15: 18 residues within 4Å: Chain G: W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, H.197, L.201, S.206, S.207 Ligands: UQ6.11 16 PLIP interactions: 16 interactions with chain G, Hydrophobic interactions: G:L.36, G:L.36, G:L.113, G:W.114, G:W.114, G:I.120, G:L.201 Hydrogen bonds: G:G.33, G:S.105, G:S.206, G:S.207 Salt bridges: G:H.96, G:K.99, G:K.99 Metal complexes: G:H.96, G:H.197 HEM.17: 18 residues within 4Å: Chain M: V.39, C.40, C.43, H.44, N.108, P.113, P.114, R.123, Y.129, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168, V.190 14 PLIP interactions: 14 interactions with chain M, Hydrophobic interactions: M:V.39, M:P.113, M:L.133, M:L.134, M:I.162, M:V.167, M:V.167, M:L.168, M:V.190 Hydrogen bonds: M:Y.129, M:Y.129, M:A.163 Salt bridges: M:R.123 Metal complexes: M:H.44

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.5: 18 residues within 4Å: Chain B: W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, F.121, F.278, A.298, L.302, F.327, F.329, F.331, F.333, Y.359 Chain I: Q.54 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:W.29, B:F.94, B:A.98, B:F.121, B:F.278, B:F.278, B:L.302, B:F.327, B:F.329, B:F.331, B:F.333, B:F.333 Hydrogen bonds: B:Y.103, I:Q.54 8PE.20: 21 residues within 4Å: Chain G: W.29, F.94, M.97, A.98, K.99, Y.102, Y.103, F.121, P.209, F.278, T.317, F.326, F.327, F.329, F.331, F.333, Y.359 Chain O: Q.54, V.58 Chain Q: E.81 Ligands: CN3.14 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain O Hydrophobic interactions: G:F.94, G:A.98, G:F.121, G:F.278, G:F.326, G:F.327, G:F.329, G:F.331, G:F.333, G:F.333, O:V.58 Salt bridges: G:K.323 Hydrogen bonds: O:Q.54, O:Q.54

1 x CN5: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate(Non-covalent)

CN5.6: 14 residues within 4Å: Chain B: Y.16, I.17, I.195, M.199 Chain G: L.12, Y.16, I.17, I.195, L.198, M.199 Ligands: 9PE.2, UQ6.11, 9PE.12, 6PH.18 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:I.195 Hydrophobic interactions: G:Y.16, G:I.17, G:I.17

2 x 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(Non-covalent)

UQ6.7: 14 residues within 4Å: Chain B: Y.16, Q.22, G.33, S.34, G.37, V.45, I.48, F.49, M.52, A.191, L.201, M.221 Ligands: 6PH.1, HEM.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.45, B:I.48, B:F.49 UQ6.11: 18 residues within 4Å: Chain B: W.164, L.182, I.189 Chain G: Y.16, I.17, G.33, S.34, G.37, V.41, I.44, I.48, F.49, V.194, L.198, M.221 Ligands: CN5.6, HEM.15, 6PH.18 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain B Hydrophobic interactions: G:V.41, G:I.44, G:I.48, G:F.49, G:V.194, B:W.164, B:L.182, B:I.189

2 x 01: methyl ~{N}-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]phenyl]-~{N}-methoxy-carbamate

01.8: 15 residues within 4Å: Chain B: I.125, A.128, F.129, Y.132, C.133, M.139, G.143, I.147, I.269, V.270, P.271, E.272, L.275, M.295, F.296 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.125, B:F.129, B:I.269, B:P.271, B:F.296 Hydrogen bonds: B:E.272 01.16: 15 residues within 4Å: Chain G: I.125, A.128, F.129, Y.132, C.133, M.139, G.143, I.147, I.269, V.270, P.271, E.272, L.275, M.295, F.296 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:I.125, G:F.129, G:I.269, G:P.271, G:F.296 Hydrogen bonds: G:E.272

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.10: 15 residues within 4Å: Chain B: M.237, A.241 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47, F.48 Chain J: Q.26 Ligands: 6PH.1 10 PLIP interactions: 3 interactions with chain D, 4 interactions with chain E, 2 interactions with chain B, 1 interactions with chain J Hydrophobic interactions: D:T.212, D:L.216, E:A.41, E:F.48, B:M.237, B:A.241 Salt bridges: D:K.211 Hydrogen bonds: E:S.43, E:T.47, J:Q.26 7PH.19: 12 residues within 4Å: Chain G: M.237, L.240 Chain M: L.208, K.211, T.212, I.215 Chain N: G.40, A.41, S.43, T.44, T.47 Chain R: Q.26 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain M, 2 interactions with chain N Hydrophobic interactions: G:L.240, M:T.212, N:A.41 Salt bridges: M:K.211 Hydrogen bonds: N:S.43

1 x 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(Non-covalent)

CN3.14: 13 residues within 4Å: Chain G: N.27, Y.28, W.29, M.95, V.231, F.236 Chain M: Y.220, I.224, K.227, K.228 Chain O: R.50 Chain Q: H.84 Ligands: 8PE.20 12 PLIP interactions: 6 interactions with chain G, 1 interactions with chain Q, 2 interactions with chain M, 3 interactions with chain O Hydrophobic interactions: G:Y.28, G:W.29, G:F.236, G:F.236 Hydrogen bonds: G:Y.28, G:Y.28, O:R.50, O:R.50 Salt bridges: Q:H.84, M:K.227, M:K.228, O:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.X. et al., Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors. J.Am.Chem.Soc. (2024)

Release Date

2024-12-25

Peptides

COR1 isoform 1: AK
Cytochrome b: BG
Cytochrome b-c1 complex subunit 2, mitochondrial: CL
quinol--cytochrome-c reductase: DM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EN
QCR6 isoform 1: FP
Cytochrome b-c1 complex subunit 7: HQ
Cytochrome b-c1 complex subunit 8: IO
Cytochrome b-c1 complex subunit 9, mitochondrial: JR
Cytochrome b-c1 complex subunit 10, mitochondrial: ST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
J

B
C

G
L

C
B

L
K

D
D

M
M

E
E

N
N

F
F

P
O

H
G

Q
P

I
H

O
Q

J
I

R
R

S
S

T
T

Membrane

We predict this structure to be a membrane protein.
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COR1 isoform 1

Cytochrome b

Cytochrome b-c1 complex subunit 2, mitochondrial

quinol--cytochrome-c reductase

Cytochrome b-c1 complex subunit Rieske, mitochondrial

QCR6 isoform 1

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9, mitochondrial

Cytochrome b-c1 complex subunit 10, mitochondrial

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