SMTL ID : 8zmt.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in Metyltetraprole-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 01: 1-[2-[[1-(4-chlorophenyl)pyrazol-3-yl]oxymethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one

01.1: 15 residues within 4Å: Chain C: I.125, A.128, F.129, Y.132, M.139, G.143, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, Y.279, M.295 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.125, C:I.269, C:P.271, C:P.271, C:Y.279 Hydrogen bonds: C:E.272 pi-Stacking: C:Y.132 01.13: 15 residues within 4Å: Chain L: I.125, A.128, F.129, Y.132, M.139, G.143, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, Y.279, M.295 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:I.125, L:I.269, L:P.271, L:P.271, L:Y.279 Hydrogen bonds: L:E.272 pi-Stacking: L:Y.132

2 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)

CN3.2: 12 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, L.35, F.88, M.91, M.95, V.231 Chain D: Y.220 Chain G: H.84 Chain H: R.50 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.28, C:L.35, C:F.88, C:F.88 Hydrogen bonds: C:Y.28, C:Y.28, D:Y.220 CN3.19: 11 residues within 4Å: Chain L: N.27, Y.28, W.29, M.32, V.231 Chain M: Y.220, I.224, K.227, K.228 Chain P: H.84 Chain Q: R.50 11 PLIP interactions: 3 interactions with chain M, 3 interactions with chain Q, 4 interactions with chain L, 1 interactions with chain P Hydrogen bonds: M:Y.220, Q:R.50, Q:R.50, L:Y.28, L:Y.28, L:Y.28 Salt bridges: M:K.227, M:K.228, Q:R.50, P:H.84 Hydrophobic interactions: L:W.29

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

9PE.3: 10 residues within 4Å: Chain C: F.3, S.6, N.7, L.10, L.12 Chain L: T.112, N.115, V.116, I.195, M.196 9 PLIP interactions: 6 interactions with chain L, 3 interactions with chain C Hydrophobic interactions: L:T.112, L:V.116, L:I.195, C:L.10, C:L.12 Hydrogen bonds: L:T.112, L:T.112, L:N.115, C:S.6 9PE.16: 10 residues within 4Å: Chain C: T.112, N.115, V.116, M.196 Chain L: F.3, N.7, Y.9, L.12, V.13, I.195 8 PLIP interactions: 3 interactions with chain L, 5 interactions with chain C Hydrophobic interactions: L:L.12, L:V.13, L:I.195, C:T.112, C:N.115, C:V.116 Hydrogen bonds: C:T.112, C:N.115

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

HEM.4: 16 residues within 4Å: Chain C: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.86, F.89, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.48, C:A.86, C:F.89, C:V.135, C:F.180, C:Y.184 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.183 HEM.5: 17 residues within 4Å: Chain C: W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, I.120, H.197, L.201, S.206, S.207 Ligands: UQ6.7 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:L.113, C:W.114, C:W.114, C:I.120, C:L.201 Hydrogen bonds: C:G.33, C:S.105, C:S.207 Salt bridges: C:H.96, C:K.99, C:K.99 Metal complexes: C:H.96, C:H.197 HEM.8: 17 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, P.113, P.114, I.119, R.123, Y.129, L.133, L.134, F.157, I.162, A.163, M.164, V.167 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:V.39, D:P.113, D:I.119, D:L.133, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167 Hydrogen bonds: D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.17: 16 residues within 4Å: Chain L: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.86, F.89, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187 12 PLIP interactions: 12 interactions with chain L, Hydrophobic interactions: L:L.40, L:Q.43, L:I.48, L:A.86, L:F.89, L:V.135, L:F.180, L:Y.184 Salt bridges: L:R.79, L:R.79 Metal complexes: L:H.82, L:H.183 HEM.20: 18 residues within 4Å: Chain L: W.30, G.33, L.36, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, I.120, V.194, H.197, L.201, S.206, S.207 Ligands: UQ6.14 15 PLIP interactions: 15 interactions with chain L, Hydrophobic interactions: L:L.36, L:L.113, L:W.114, L:I.120, L:V.194, L:V.194, L:L.201 Hydrogen bonds: L:G.33, L:S.105, L:S.207 Salt bridges: L:H.96, L:K.99, L:K.99 Metal complexes: L:H.96, L:H.197 HEM.21: 17 residues within 4Å: Chain M: V.39, C.40, C.43, H.44, N.108, P.113, P.114, I.119, R.123, Y.129, L.133, L.134, F.157, I.162, A.163, M.164, V.167 14 PLIP interactions: 14 interactions with chain M, Hydrophobic interactions: M:V.39, M:P.113, M:I.119, M:L.133, M:L.134, M:L.134, M:I.162, M:A.163, M:M.164, M:V.167 Hydrogen bonds: 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.6: 9 residues within 4Å: Chain C: W.29, M.97, A.98, Y.102, Y.103, F.121, F.278, F.333, Y.359 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.29, C:W.29, C:F.121, C:F.278, C:F.333 Hydrogen bonds: C:Y.102, C:Y.103, C:Y.103 8PE.15: 10 residues within 4Å: Chain L: W.29, F.94, M.97, A.98, Y.102, Y.103, F.327, F.333 Chain Q: Q.54, V.58 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:W.29, L:W.29, L:F.94, L:Y.102, L:F.333 Hydrogen bonds: L:Y.102, L:Y.103, L:Y.103

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 C: Y.16, I.17, G.33, S.34, G.37, L.40, A.191, L.198, L.201, M.221, D.229 Chain E: M.52 Ligands: HEM.5, 6PH.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.17, C:L.40, C:A.191, C:L.198 Hydrogen bonds: C:S.34 UQ6.14: 13 residues within 4Å: Chain C: W.164 Chain L: Y.16, S.34, L.40, V.45, F.49, L.198, L.201, M.221, D.229 Ligands: 6PH.12, CN5.18, HEM.20 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:L.40, L:V.45, L:F.49, C:W.164 Hydrogen bonds: L:D.229

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

6PH.9: 15 residues within 4Å: Chain C: I.42, L.81, M.237, L.240 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47 Ligands: 6PH.11 7 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:L.216, C:I.42, C:L.81, C:L.240, E:A.41, E:T.44 Salt bridges: D:K.211 6PH.11: 12 residues within 4Å: Chain A: S.424, M.429 Chain C: S.34, H.222, S.223, I.226, D.229 Chain E: V.30, M.33, S.37 Ligands: UQ6.7, 6PH.9 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.226, C:I.226, C:D.229 Hydrogen bonds: C:S.223, C:S.223, A:S.424 Salt bridges: C:H.222, C:H.222 6PH.12: 11 residues within 4Å: Chain J: S.424, M.429 Chain L: S.34, H.222, S.223, D.229, L.230 Chain N: V.30, M.33 Ligands: UQ6.14, CN5.18 7 PLIP interactions: 5 interactions with chain L, 1 interactions with chain J, 1 interactions with chain N Hydrophobic interactions: L:D.229, L:L.230, N:V.30 Hydrogen bonds: L:S.223, J:S.424 Salt bridges: L:H.222, L:H.222

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.10: 7 residues within 4Å: Chain E: H.131, C.134, C.148, H.151, S.153, P.165, A.166 0 PLIP interactions: FES.22: 6 residues within 4Å: Chain N: H.131, C.134, H.151, S.153, P.165, A.166 0 PLIP interactions:

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)

CN5.18: 12 residues within 4Å: Chain C: L.12, Y.16, M.199 Chain L: L.12, Y.16, I.17, I.195, L.198, M.199, H.222 Ligands: 6PH.12, UQ6.14 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:I.17, C:L.12 Hydrogen bonds: L:Y.16

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: AJ
Cytochrome b-c1 complex subunit 2, mitochondrial: BK
Cytochrome b: CL
Cytochrome c1, heme protein, mitochondrial: DM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EN
Cytochrome b-c1 complex subunit 6, mitochondrial: FO
Cytochrome b-c1 complex subunit 7: GP
Cytochrome b-c1 complex subunit 8: HQ
Cytochrome b-c1 complex subunit 9, mitochondrial: IR
Cytochrome b-c1 complex subunit 10, mitochondrial: ST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
L

B
B

K
M

C
C

L
N

D
D

M
O

E
E

N
P

F
F

O
Q

G
G

P
R

H
H

Q
S

I
I

R
T

S
U

T
V

Membrane

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

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 6, mitochondrial

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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