SMTL ID : 8yio.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-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 AZO: METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE(Non-covalent)

AZO.1: 18 residues within 4Å: Chain B: I.125, A.128, F.129, Y.132, C.133, S.140, G.143, A.144, I.147, V.270, P.271, E.272, Y.274, L.275, F.278, M.295, F.296, I.299 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.125, B:Y.132, B:I.147, B:P.271, B:L.275, B:F.278, B:I.299 Hydrogen bonds: B:E.272 pi-Stacking: B:F.296 AZO.10: 18 residues within 4Å: Chain E: I.125, A.128, F.129, Y.132, C.133, S.140, G.143, A.144, I.147, V.270, P.271, E.272, Y.274, L.275, F.278, M.295, F.296, I.299 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.125, E:Y.132, E:I.147, E:P.271, E:L.275, E:F.278, E:I.299 Hydrogen bonds: E:E.272 pi-Stacking: E:F.296

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)

UQ6.2: 17 residues within 4Å: Chain B: Y.16, I.17, Q.22, S.34, G.37, I.44, V.45, F.49, V.194, L.198, L.201, S.206, M.221 Chain E: L.182, L.185 Chain F: M.52 Ligands: HEM.8 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:I.44, B:V.45, B:F.49, B:V.194, B:L.198, E:L.182, E:L.185 Hydrogen bonds: B:Y.16, B:Q.22 UQ6.17: 19 residues within 4Å: Chain B: L.185 Chain E: Y.16, Q.22, G.33, S.34, G.37, I.44, I.48, F.49, M.52, A.191, L.198, L.201, S.206, M.221, D.229 Ligands: CN5.6, 6PH.11, HEM.15 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:I.44, E:I.48, E:F.49, E:A.191, E:L.198, B:L.185 Hydrogen bonds: E:Q.22

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

8PE.3: 15 residues within 4Å: Chain B: W.29, F.94, A.98, Y.102, Y.103, P.209, T.317, F.326, F.327, F.333, Y.359 Chain H: E.81 Chain I: F.51, Q.54 Ligands: CN3.7 7 PLIP interactions: 1 interactions with chain I, 6 interactions with chain B Hydrogen bonds: I:Q.54, B:P.209 Hydrophobic interactions: B:W.29, B:W.29, B:A.98, B:Y.102, B:F.333 8PE.16: 10 residues within 4Å: Chain E: W.29, K.99, Y.102, Y.103, F.121, K.323, Y.359 Chain Q: F.51, Q.54 Ligands: CN3.12 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain Q Hydrophobic interactions: E:F.121, Q:F.51 Hydrogen bonds: E:K.323, E:K.323

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

9PE.4: 11 residues within 4Å: Chain B: F.3, S.6, N.7, V.8, Y.9, L.10 Chain E: T.112, N.115, A.192, I.195, M.196 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: E:T.112, E:A.192, E:I.195, B:Y.9, B:L.10 Hydrogen bonds: E:N.115, B:N.7, B:V.8 9PE.13: 9 residues within 4Å: Chain B: T.112, N.115, M.196 Chain E: F.3, S.6, N.7, V.8, L.10 Ligands: CN5.6 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.10, B:T.112 Hydrogen bonds: E:N.7, E:V.8, B:N.115

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

HEM.5: 16 residues within 4Å: Chain B: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, T.127, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.40, B:Q.43, B:I.48, B:T.127, B:Y.184 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.82 HEM.8: 19 residues within 4Å: Chain B: W.30, G.33, L.36, G.37, 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: UQ6.2 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:L.36, B:L.36, B:L.113, B:W.114, B:W.114, B:I.120, B:V.194, B:L.201 Hydrogen bonds: B:G.33, B:S.105, 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, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.39, D:P.113, D:I.119, D:I.130, D:L.133, D:L.134, D:I.162, D:A.163, D:V.167, D:V.167 Hydrogen bonds: D:Y.129, D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.14: 16 residues within 4Å: Chain E: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, T.127, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 8 PLIP interactions: 8 interactions with chain E, Hydrophobic interactions: E:L.40, E:Q.43, E:I.48, E:T.127, E:Y.184 Salt bridges: E:R.79, E:R.79 Metal complexes: E:H.82 HEM.15: 19 residues within 4Å: Chain E: W.30, G.33, L.36, G.37, 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: UQ6.17 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:L.36, E:L.36, E:L.113, E:W.114, E:W.114, E:I.120, E:V.194, E:L.201 Hydrogen bonds: E:G.33, E:S.105, E:S.207 Salt bridges: E:H.96, E:K.99, E:K.99, E:R.110 Metal complexes: E:H.96, E:H.197 HEM.19: 18 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, I.130, 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:I.130, M:L.133, M:L.134, M:I.162, M:A.163, M:V.167, M:V.167 Hydrogen bonds: 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: 12 residues within 4Å: Chain B: L.12, Y.16, I.17, I.18, L.198, M.199 Chain E: L.12, Y.16, L.198, M.199 Ligands: 9PE.13, UQ6.17 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:Y.16, B:I.17, B:I.18, E:Y.16, E:L.198

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)

CN3.7: 13 residues within 4Å: Chain B: N.27, Y.28, W.29, M.32, L.235, F.236 Chain D: Y.220, I.224, K.227, K.228 Chain H: H.84 Chain I: R.50 Ligands: 8PE.3 11 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H, 3 interactions with chain I, 5 interactions with chain B Salt bridges: D:K.227, D:K.228, H:H.84, I:R.50 Hydrogen bonds: I:R.50, I:R.50, B:Y.28, B:Y.28 Hydrophobic interactions: B:Y.28, B:W.29, B:F.236 CN3.12: 18 residues within 4Å: Chain E: N.27, Y.28, W.29, M.32, F.88, M.91, M.95, V.231, F.236 Chain M: Y.220, I.224, K.227, K.228, W.231, K.235 Chain P: H.84 Chain Q: R.50 Ligands: 8PE.16 15 PLIP interactions: 3 interactions with chain E, 2 interactions with chain Q, 1 interactions with chain P, 9 interactions with chain M Hydrophobic interactions: E:F.88, E:F.236, E:F.236, M:K.228, M:W.231, M:K.235 Hydrogen bonds: Q:R.50 Salt bridges: Q:R.50, P:H.84, M:K.227, M:K.227, M:K.228, M:K.228, M:K.235, M:K.235

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

6PH.11: 13 residues within 4Å: Chain E: H.222, I.226, D.229, L.230, F.234 Chain K: S.424, M.429 Chain N: V.30, M.33, S.37 Chain R: F.14 Ligands: UQ6.17, 6PH.18 6 PLIP interactions: 1 interactions with chain R, 1 interactions with chain K, 4 interactions with chain E Hydrophobic interactions: R:F.14, E:I.226, E:L.230, E:F.234 Hydrogen bonds: K:S.424 Salt bridges: E:H.222 6PH.18: 12 residues within 4Å: Chain E: M.237, A.241 Chain M: L.208, K.211, T.212, L.216 Chain N: S.37, G.40, A.41, S.43, T.44 Ligands: 6PH.11 7 PLIP interactions: 2 interactions with chain N, 3 interactions with chain M, 2 interactions with chain E Hydrophobic interactions: N:A.41, M:T.212, M:L.216, E:M.237, E:A.241 Hydrogen bonds: N:S.43 Salt bridges: M:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, Y. et al., Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state. To Be Published

Release Date

2025-03-05

Peptides

COR1 isoform 1: AK
Cytochrome b: BE
Cytochrome b-c1 complex subunit 2, mitochondrial: CL
Cytochrome c1, heme protein, mitochondrial: DM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: FN
QCR6 isoform 1: GO
Cytochrome b-c1 complex subunit 7: HP
Cytochrome b-c1 complex subunit 8: 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

E
N

C
B

L
M

D
D

M
O

F
E

N
P

G
F

O
Q

H
G

P
R

I
H

Q
S

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

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

Related Entries With Identical Sequence