SMTL ID : 8zjc.1

Cryo-EM structure of Saccharomyces cerevisiae bc1 complex

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: 16 residues within 4Å: Chain C: Y.16, Q.22, G.33, S.34, G.37, V.41, I.44, V.45, V.194, L.198, M.221, D.229 Chain E: M.52 Chain L: L.182 Ligands: CN5.6, HEM.8 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: C:V.41, C:I.44, C:V.45, C:V.194, L:L.182 Hydrogen bonds: C:Q.22, C:D.229 UQ6.16: 18 residues within 4Å: Chain C: L.182, L.185 Chain L: Y.16, Q.22, G.33, S.34, G.37, V.41, I.44, I.48, F.49, M.52, V.194, L.198, L.201, M.221 Ligands: 6PH.11, HEM.14 8 PLIP interactions: 6 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:V.41, L:I.44, L:I.48, L:F.49, L:V.194, C:L.182, C:L.185 Hydrogen bonds: L:Q.22

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

8PE.2: 14 residues within 4Å: Chain C: W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, T.317, V.330, Y.359 Chain H: Q.54, V.58 Ligands: CN3.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:F.94, C:V.330, H:V.58 Hydrogen bonds: C:Y.102 8PE.15: 12 residues within 4Å: Chain L: N.27, W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, F.326 Chain P: E.81 Chain Q: Q.54 11 PLIP interactions: 9 interactions with chain L, 1 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: L:W.29, L:W.29, L:F.94, L:A.98, L:Y.102, L:Y.103, L:F.326 Hydrogen bonds: L:N.27, L:Y.103, Q:Q.54, P:E.81

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, N.7, Y.9, L.10 Chain L: T.112, N.115, V.116, I.119, M.193, M.196 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:V.116, L:I.119, C:Y.9 Hydrogen bonds: C:N.7 9PE.4: 9 residues within 4Å: Chain C: T.112, N.115, I.195, M.196 Chain L: F.3, N.7, Y.9, L.10, L.12 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:Y.9, L:L.10, L:L.12, C:I.195 Hydrogen bonds: L:N.7, C:N.115

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

HEM.5: 16 residues within 4Å: Chain C: L.40, Q.43, G.47, I.48, M.50, R.79, H.82, A.83, F.89, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.48, C:A.83, C:F.89, C:Y.184, C:Y.184, C:P.187 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.183 HEM.8: 20 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, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.1 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:L.113, C:W.114, C:I.120, C:V.194, C:L.198, C:L.201 Hydrogen bonds: C:W.30, C:G.33, C:S.105, 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.9: 18 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, L.112, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, V.190 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:I.119, D:I.130, D:L.133, D:L.134, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167, D:V.167, D:V.190 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.13: 17 residues within 4Å: Chain L: L.40, Q.43, G.47, I.48, M.50, A.51, R.79, H.82, A.83, F.89, G.131, Y.132, V.135, H.183, Y.184, P.187, Y.274 11 PLIP interactions: 11 interactions with chain L, Hydrophobic interactions: L:L.40, L:Q.43, L:A.51, L:A.83, L:F.89, L:Y.184, L:P.187 Salt bridges: L:R.79, L:R.79 Metal complexes: L:H.82, L:H.183 HEM.14: 20 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, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.16 17 PLIP interactions: 17 interactions with chain L, Hydrophobic interactions: L:L.36, L:L.36, L:L.113, L:W.114, L:I.120, L:V.194, L:L.198, L:L.201 Hydrogen bonds: L:W.30, 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.17: 18 residues within 4Å: Chain M: V.39, C.40, C.43, H.44, N.108, L.112, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167 12 PLIP interactions: 12 interactions with chain M, Hydrophobic interactions: M:I.119, M:I.130, M:L.133, M:L.134, M:I.162, M:A.163, M:M.164, M:V.167, M:V.167 Hydrogen bonds: 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: 10 residues within 4Å: Chain C: L.12, Y.16, I.195, L.198, M.199 Chain L: L.12, Y.16, A.192, M.199 Ligands: UQ6.1 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:L.12, L:Y.16, L:Y.16, L:A.192 Hydrogen bonds: C:Y.16

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: 11 residues within 4Å: Chain C: N.27, Y.28, W.29, M.32, M.95, V.231, F.236 Chain D: Y.220 Chain G: H.84 Chain H: R.50 Ligands: 8PE.2 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:Y.28, C:W.29, C:F.236 Hydrogen bonds: H:R.50 Salt bridges: H:R.50, G:H.84 CN3.12: 13 residues within 4Å: Chain L: N.27, Y.28, W.29, M.32, F.88, V.231, F.236 Chain M: Y.220, I.224, K.227, K.228 Chain P: H.84 Chain Q: R.50 10 PLIP interactions: 3 interactions with chain Q, 4 interactions with chain L, 1 interactions with chain P, 2 interactions with chain M Hydrogen bonds: Q:R.50, Q:R.50, L:Y.28 Salt bridges: Q:R.50, P:H.84, M:K.227, M:K.228 Hydrophobic interactions: L:F.88, L:V.231, L:F.236

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

FES.10: 6 residues within 4Å: Chain E: H.131, C.148, G.152, S.153, Y.155, A.166 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:H.131, E:Y.155 FES.18: 9 residues within 4Å: Chain N: H.131, C.134, C.148, C.150, H.151, G.152, S.153, Y.155, A.166 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:H.131, N:C.148, N:Y.155

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

6PH.11: 8 residues within 4Å: Chain J: S.424, M.429 Chain L: H.222, D.229, L.230 Chain N: V.30 Ligands: UQ6.16, 6PH.19 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: L:D.229, L:L.230, N:V.30 Salt bridges: M:K.230 6PH.19: 17 residues within 4Å: Chain L: I.42, L.81, M.237, L.240 Chain M: L.208, K.211, T.212, I.215, L.216, L.219 Chain N: S.37, G.40, S.43, T.44, E.46, T.47 Ligands: 6PH.11 14 PLIP interactions: 7 interactions with chain M, 4 interactions with chain L, 3 interactions with chain N Hydrophobic interactions: M:T.212, M:I.215, M:I.215, M:L.216, M:L.219, L:I.42, L:L.81, L:M.237, L:L.240 Salt bridges: M:K.211, M:K.211 Hydrogen bonds: N:S.43, N:S.43, N:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-05-21

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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