SMTL ID : 8yil.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-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 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)

UQ6.1: 17 residues within 4Å: Chain B: Y.16, I.17, S.34, I.44, V.45, F.49, A.191, V.194, I.195, L.198, L.201, M.221 Chain F: W.164, L.182, L.185 Ligands: CN5.5, HEM.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:I.44, B:V.45, B:F.49, B:V.194, B:I.195, F:L.182, F:L.185 UQ6.15: 12 residues within 4Å: Chain F: Y.16, I.17, Q.22, S.34, V.45, I.48, A.191, V.194, L.198, L.201, M.221 Ligands: HEM.14 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.17, F:V.45, F:I.48, F:A.191, F:V.194, F:L.198

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

8PE.2: 12 residues within 4Å: Chain B: W.29, F.94, M.97, A.98, Y.102, Y.103, T.317, F.326, F.333, Y.359 Chain I: Q.54 Ligands: CN3.7 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:W.29, B:F.94, B:A.98, B:F.333 Hydrogen bonds: B:Y.102, I:Q.54 8PE.18: 13 residues within 4Å: Chain F: W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, F.333, Y.359 Chain N: Q.54 Chain Q: E.81 Ligands: CN3.11 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: F:F.94, F:F.333 Hydrogen bonds: F:Y.103, N:Q.54, Q:E.81, Q:E.81

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

9PE.3: 9 residues within 4Å: Chain B: F.3, S.6, N.7, V.8, V.13 Chain F: T.112, N.115, I.195, I.203 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:I.195, B:V.13 Hydrogen bonds: F:T.112, F:N.115, B:N.7, B:V.8 9PE.12: 7 residues within 4Å: Chain B: T.112, N.115, M.196 Chain F: F.3, S.6, N.7, Y.9 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:Y.9 Hydrogen bonds: F:S.6, F:N.7, B:T.112, B:T.112, B:N.115

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

HEM.4: 18 residues within 4Å: Chain B: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, A.86, F.89, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.40, B:Q.43, B:I.48, B:A.86, B:F.89, B:T.127, B:V.135, B:F.180, B:Y.184, B:Y.184 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.82, B:H.183 HEM.8: 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, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.1 19 PLIP interactions: 19 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.198, B:L.201 Hydrogen bonds: B:W.30, B:G.33, B:S.105, B:S.206, 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, P.113, P.114, 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 D, Hydrophobic interactions: D:P.113, D:I.130, D:L.133, D:L.134, D:L.134, D:I.162, D:M.164, D:V.167 Hydrogen bonds: D:Y.129, D:Y.129, D:A.163 Salt bridges: D:R.123 pi-Stacking: D:H.44 Metal complexes: D:H.44 HEM.13: 18 residues within 4Å: Chain F: L.40, Q.43, G.47, M.50, A.51, R.79, H.82, A.83, A.86, F.89, T.127, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:L.40, F:Q.43, F:A.51, F:A.86, F:F.89, F:T.127, F:V.135, F:F.180, F:Y.184, F:Y.184 Salt bridges: F:R.79, F:R.79 Metal complexes: F:H.82, F:H.183 HEM.14: 18 residues within 4Å: Chain F: 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: UQ6.15 16 PLIP interactions: 16 interactions with chain F, Hydrophobic interactions: F:L.36, F:L.36, F:L.113, F:W.114, F:W.114, F:I.120, F:V.194, F:L.201 Hydrogen bonds: F:G.33, F:S.105, F:S.207 Salt bridges: F:H.96, F:K.99, F:K.99 Metal complexes: F:H.96, F:H.197 HEM.16: 17 residues within 4Å: Chain L: V.39, C.40, C.43, H.44, N.108, P.113, P.114, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167 11 PLIP interactions: 11 interactions with chain L, Hydrophobic interactions: L:V.39, L:P.113, L:I.130, L:L.134, L:I.162, L:M.164, L:V.167 Hydrogen bonds: L:Y.129, L:A.163 Salt bridges: L:R.123 Metal complexes: L: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)

CN5.5: 14 residues within 4Å: Chain B: L.12, V.13, Y.16, I.17, I.195, L.198, M.199, I.226, D.229, L.230 Chain F: L.12, Y.16, M.199 Ligands: UQ6.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.195, B:I.226 Hydrogen bonds: B:Y.16

2 x 86T: metyltetraprole(Non-covalent)

86T.6: 15 residues within 4Å: Chain B: I.125, A.128, F.129, Y.132, G.143, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, Y.279, M.295, F.296 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.125, B:I.269, B:P.271, B:Y.279 Hydrogen bonds: B:E.272 pi-Stacking: B:Y.132 86T.10: 15 residues within 4Å: Chain F: I.125, A.128, F.129, Y.132, G.143, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, Y.279, M.295, F.296 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.125, F:I.269, F:P.271, F:Y.279 Hydrogen bonds: F:E.272 pi-Stacking: F: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)

CN3.7: 13 residues within 4Å: Chain B: N.27, Y.28, W.29, M.32, V.231, F.236 Chain D: Y.220, I.224, K.227, K.228 Chain H: H.84 Chain I: R.50 Ligands: 8PE.2 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain B, 2 interactions with chain D, 1 interactions with chain H Hydrogen bonds: I:R.50, I:R.50, B:Y.28, B:Y.28 Salt bridges: I:R.50, D:K.227, D:K.228, H:H.84 Hydrophobic interactions: B:W.29, B:F.236 CN3.11: 13 residues within 4Å: Chain F: N.27, Y.28, W.29, M.32, V.231, L.235 Chain L: Y.220, I.224, K.227, K.228 Chain N: R.50 Chain Q: H.84 Ligands: 8PE.18 10 PLIP interactions: 3 interactions with chain F, 3 interactions with chain L, 2 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: F:W.29, F:L.235, L:I.224 Hydrogen bonds: F:Y.28, N:N.42, Q:H.84 Salt bridges: L:K.227, L:K.228, N:R.50, Q:H.84

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

6PH.17: 11 residues within 4Å: Chain F: I.42, L.81, M.237 Chain L: K.211, T.212, I.215, L.216 Chain O: G.40, A.41, S.43, T.44 9 PLIP interactions: 5 interactions with chain L, 2 interactions with chain F, 2 interactions with chain O Hydrophobic interactions: L:T.212, L:I.215, L:L.216, F:I.42, F:L.81, O:A.41 Salt bridges: L:K.211, L:K.211 Hydrogen bonds: O:S.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, Y. et al., Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-bound state. To Be Published

Release Date

2025-03-05

Peptides

COR1 isoform 1: AK
Cytochrome b: BF
Cytochrome b-c1 complex subunit 2, mitochondrial: CM
Cytochrome c1, heme protein, mitochondrial: DL
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
QCR6 isoform 1: GP
Cytochrome b-c1 complex subunit 7: HQ
Cytochrome b-c1 complex subunit 8: IN
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

F
N

C
B

M
M

D
D

L
O

E
E

O
P

G
F

P
Q

H
G

Q
R

I
H

N
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