SMTL ID : 8yin.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-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: 11 residues within 4Å: Chain A: S.424, S.427, M.428, M.429, R.430 Chain B: I.18, H.222, I.226, F.227, L.230 Ligands: CN5.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.18, B:I.226, B:F.227, B:F.227 Salt bridges: B:H.222 6PH.10: 13 residues within 4Å: Chain B: I.42, L.81, M.237, L.240 Chain D: K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47 10 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: D:L.216, D:L.216, B:I.42, B:L.81, B:M.237, B:L.240, E:A.41, E:T.44 Salt bridges: D:K.211 Hydrogen bonds: E:T.47

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: 14 residues within 4Å: Chain B: N.27, Y.28, W.29, M.32, M.95, V.231, T.232 Chain D: Y.220, I.224, K.227, K.228 Chain F: R.50 Chain I: H.84 Ligands: 8PE.11 9 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B, 1 interactions with chain I, 2 interactions with chain F Salt bridges: D:K.227, D:K.228, I:H.84, F:R.50 Hydrophobic interactions: B:W.29 Hydrogen bonds: B:N.27, B:Y.28, B:Y.28, F:R.50 CN3.12: 13 residues within 4Å: Chain G: N.27, Y.28, W.29, M.32, M.95, V.231, T.232 Chain M: Y.220, I.224, K.227 Chain N: R.50 Chain Q: H.84 Ligands: 8PE.19 8 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M, 3 interactions with chain G, 1 interactions with chain Q Hydrogen bonds: N:R.50, N:R.50, G:N.27, G:Y.28, G:Y.28 Salt bridges: N:R.50, M:K.227, Q:H.84

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 B: F.3, N.7, Y.9, V.13 Chain G: T.112, N.115, A.192, I.195, M.196 Ligands: CN5.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain G Hydrophobic interactions: B:Y.9, B:V.13, G:T.112, G:N.115, G:I.195 Hydrogen bonds: B:N.7, G:N.115 9PE.15: 10 residues within 4Å: Chain B: T.112, N.115, V.116, I.119, M.196 Chain G: N.7, Y.9, L.10, L.12 Ligands: CN5.6 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Hydrophobic interactions: G:L.10, G:L.12, B:I.119 Hydrogen bonds: G:N.7, B:N.115

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

HEM.4: 17 residues within 4Å: Chain B: L.40, Q.43, G.47, M.50, A.51, R.79, H.82, A.86, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.40, B:A.51, B:A.86, B:V.135, B:F.180, B:Y.184, B:P.187 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.183 HEM.5: 19 residues within 4Å: Chain B: 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, 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:V.194, B:L.201 Hydrogen bonds: B:G.33, B:S.105, B:S.105, B:S.207 Salt bridges: B:H.96, B:K.99, B:K.99 Metal complexes: B:H.96, B:H.197 HEM.9: 16 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:V.39, D:I.119, D:I.130, D:L.133, D:L.134, D:L.134, D:I.162, D:M.164, D:V.167, D:L.168 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.13: 19 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, V.194, H.197, L.201, S.206, S.207 Ligands: UQ6.14 16 PLIP interactions: 16 interactions with chain G, Hydrophobic interactions: G:L.36, G:L.36, G:L.113, G:W.114, G:I.120, G:V.194, G:V.194, G:L.201 Hydrogen bonds: G:G.33, G:S.105, G:S.207 Salt bridges: G:H.96, G:K.99, G:K.99 Metal complexes: G:H.96, G:H.197 HEM.16: 17 residues within 4Å: Chain G: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.86, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 11 PLIP interactions: 11 interactions with chain G, Hydrophobic interactions: G:L.40, G:I.48, G:A.86, G:V.135, G:F.180, G:Y.184, G:Y.184, G:P.187 Salt bridges: G:R.79, G:R.79 Metal complexes: G:H.183 HEM.18: 16 residues within 4Å: Chain M: V.39, C.40, C.43, H.44, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:V.39, M:I.119, M:I.130, M:L.133, M:L.134, M:L.134, M:I.162, M:M.164, M:V.167, M:L.168 Hydrogen bonds: M:Y.129, M:Y.129, M:A.163 Salt bridges: M:R.123 Metal complexes: M:H.44

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: L.12, Y.16, I.17, M.199 Chain G: L.12, Y.16, I.17, I.195, M.199 Ligands: 6PH.1, 9PE.3, UQ6.7, UQ6.14, 9PE.15 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:Y.16, G:Y.16, G:I.17, G:I.17, G:I.195 Hydrogen bonds: B:Y.16

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, I.17, Q.22, S.34, G.37, I.44, V.45, I.48, F.49, L.198, L.201, M.221 Ligands: HEM.5, CN5.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.17, B:I.44, B:V.45, B:I.48, B:F.49 Hydrogen bonds: B:Y.16, B:Q.22 UQ6.14: 16 residues within 4Å: Chain G: Y.16, I.17, Q.22, G.33, S.34, G.37, L.40, I.48, F.49, M.52, L.198, L.201, S.206, M.221 Ligands: CN5.6, HEM.13 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.40, G:I.48, G:F.49, G:L.198 Hydrogen bonds: G:Y.16, G:Q.22

2 x 01: 1-[2-[(4,6-dimethyl-1,3-benzothiazol-2-yl)sulfanylmethyl]-3-methyl-phenyl]-4-methyl-1,2,3,4-tetrazol-5-one

01.8: 15 residues within 4Å: Chain B: I.125, A.128, F.129, Y.132, M.139, G.143, I.147, I.269, V.270, P.271, E.272, L.275, Y.279, M.295, F.296 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.125, B:F.129, B:I.269, B:P.271, B:Y.279, B:F.296 Hydrogen bonds: B:E.272 01.17: 14 residues within 4Å: Chain G: I.125, A.128, F.129, Y.132, G.143, I.147, I.269, V.270, P.271, E.272, L.275, Y.279, M.295, F.296 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.125, G:F.129, G:I.269, G:P.271, G:Y.279, G:F.296 Hydrogen bonds: G:E.272

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

8PE.11: 15 residues within 4Å: Chain B: W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, F.121, L.302, F.333, Y.359 Chain F: R.50, Q.54 Ligands: CN3.2 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:Q.54 Hydrophobic interactions: B:W.29, B:F.94, B:F.121, B:L.302, B:F.333 8PE.19: 17 residues within 4Å: Chain G: N.27, W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, F.121, T.317, F.326, F.333, Y.359 Chain N: Q.54 Chain Q: E.81 Ligands: CN3.12 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain N Hydrophobic interactions: G:W.29, G:F.94, G:F.121, G:F.326, G:F.333 Hydrogen bonds: G:N.27, G:T.317, N:Q.54, N:Q.54

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
Cytochrome c1, heme protein, mitochondrial: DM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 8: FN
QCR6 isoform 1: HP
Cytochrome b-c1 complex subunit 7: IQ
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
L

B
C

G
N

C
B

L
M

D
D

M
O

E
E

O
P

F
H

N
S

H
F

P
Q

I
G

Q
R

J
I

R
T

S
U

T
V

Membrane

We predict this structure to be a membrane protein.
Show / Hide

COR1 isoform 1

Cytochrome b

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 8

QCR6 isoform 1

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 9, mitochondrial

Cytochrome b-c1 complex subunit 10, mitochondrial

Related Entries With Identical Sequence