SMTL ID : 6giq.1

Saccharomyces cerevisiae respiratory supercomplex III2IV

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

6PH.1: 15 residues within 4Å: Chain A: S.450, M.455 Chain C: L.38, H.222, S.223, I.226, F.227, L.230, V.233 Chain D: K.291 Chain E: M.63, S.67 Ligands: UQ6.6, 7PH.8, PCF.10 9 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:L.38, C:F.227, C:L.230, C:V.233 Hydrogen bonds: C:S.223, A:S.450 Salt bridges: C:H.222, C:H.222, D:K.291 6PH.12: 19 residues within 4Å: Chain J: S.450, M.455 Chain L: S.34, L.38, H.222, S.223, I.226, F.227, D.229, L.230, V.233, F.234 Chain M: K.291 Chain N: M.63, S.67 Ligands: CN5.5, UQ6.15, 7PH.20, PCF.22 11 PLIP interactions: 9 interactions with chain L, 1 interactions with chain M, 1 interactions with chain J Hydrophobic interactions: L:L.38, L:F.227, L:D.229, L:V.233, L:V.233, L:F.234 Hydrogen bonds: L:S.223, J:S.450 Salt bridges: L:H.222, L:H.222, M:K.291

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

HEM.2: 22 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, N.256, Y.274 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.44, C:A.51, C:A.83, C:T.127, C:F.180, C:Y.184 Hydrogen bonds: C:N.256 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.183 HEM.3: 20 residues within 4Å: Chain C: W.30, G.33, L.36, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.6 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:L.113, C:W.114, C:W.114, C:V.118, C:I.120, C:F.121, C:L.198, C:L.201 Hydrogen bonds: C:G.33, C:S.207 Salt bridges: C:H.96, C:K.99, C:R.110 Metal complexes: C:H.96, C:H.197 HEM.7: 17 residues within 4Å: Chain D: V.100, C.101, C.104, H.105, L.173, P.174, P.175, L.177, R.184, Y.190, I.191, L.194, F.218, I.223, A.224, M.225, V.228 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:V.100, D:P.174, D:P.174, D:L.177, D:I.191, D:A.224, D:V.228, D:V.228 Hydrogen bonds: D:A.224 Salt bridges: D:R.184 Metal complexes: D:H.105 HEM.13: 22 residues within 4Å: Chain L: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, R.79, H.82, A.83, A.86, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, N.256, Y.274 13 PLIP interactions: 13 interactions with chain L, Hydrophobic interactions: L:L.40, L:Q.43, L:I.44, L:A.51, L:A.83, L:T.127, L:F.180, L:Y.184 Hydrogen bonds: L:N.256 Salt bridges: L:R.79, L:R.79 Metal complexes: L:H.82, L:H.183 HEM.14: 21 residues within 4Å: Chain L: W.30, G.33, L.36, G.37, 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: UQ6.15 15 PLIP interactions: 15 interactions with chain L, Hydrophobic interactions: L:L.36, L:L.36, L:L.113, L:W.114, L:I.120, L:L.198, L:L.201 Hydrogen bonds: L:G.33, L:S.105, L:S.105, L:S.207 Salt bridges: L:H.96, L:K.99, L:R.110 Metal complexes: L:H.197 HEM.19: 15 residues within 4Å: Chain M: V.100, C.101, C.104, H.105, L.173, P.174, P.175, R.184, Y.190, I.191, L.194, L.195, F.218, A.224, M.225 10 PLIP interactions: 10 interactions with chain M, Hydrophobic interactions: M:V.100, M:P.174, M:P.175, M:I.191, M:L.194, M:L.195 Hydrogen bonds: M:Y.190, M:A.224 Salt bridges: M:R.184 Metal complexes: M:H.105

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

8PE.4: 18 residues within 4Å: Chain C: W.29, F.94, M.95, M.97, A.98, Y.102, Y.103, F.278, L.302, T.317, F.326, F.327, V.330, F.331, F.333, Y.359 Chain G: E.82 Chain H: Q.55 12 PLIP interactions: 10 interactions with chain C, 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: C:W.29, C:W.29, C:A.98, C:F.278, C:L.302, C:F.326, C:F.331, C:F.333, C:F.333 Hydrogen bonds: C:Y.102, H:Q.55, G:E.82 8PE.16: 18 residues within 4Å: Chain L: W.29, F.94, M.95, M.97, A.98, Y.102, Y.103, L.302, T.317, F.327, V.330, F.331, F.333, Y.359 Chain P: E.82 Chain Q: Q.55, V.59 Ligands: CN3.18 11 PLIP interactions: 9 interactions with chain L, 2 interactions with chain Q Hydrophobic interactions: L:W.29, L:F.94, L:A.98, L:L.302, L:L.302, L:F.331, L:F.333, Q:V.59 Hydrogen bonds: L:Y.102, L:Y.103, Q:Q.55

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: 13 residues within 4Å: Chain C: L.12, Y.16, M.199, H.202 Chain L: L.12, Y.16, I.17, I.195, M.199 Ligands: 9PE.11, 6PH.12, UQ6.15, 9PE.17 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: L:Y.16 Hydrogen bonds: L:Y.16, C:Y.16 Salt bridges: C:H.202

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)

UQ6.6: 14 residues within 4Å: Chain C: Y.16, I.17, Q.22, S.34, V.41, I.44, F.49, L.201, S.206, M.221, D.229 Chain L: L.182 Ligands: 6PH.1, HEM.3 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: C:Y.16, C:I.17, C:I.44, C:I.44, C:F.49, C:F.49, L:L.182 Hydrogen bonds: C:Y.16, C:Q.22, C:D.229 UQ6.15: 15 residues within 4Å: Chain L: Y.16, I.17, S.34, G.37, I.44, I.48, F.49, V.194, L.198, L.201, M.221, D.229 Ligands: CN5.5, 6PH.12, HEM.14 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:I.17, L:I.44, L:I.48, L:F.49, L:F.49, L:V.194, L:L.198

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.8: 16 residues within 4Å: Chain C: I.42, I.77, L.81, M.237, L.240, F.245 Chain D: L.269, K.272, T.273, I.276, L.277 Chain E: G.70, S.73, E.76, F.78 Ligands: 6PH.1 9 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: D:T.273, D:L.277, E:F.78, C:I.42, C:I.42, C:L.240 Salt bridges: D:K.272 Hydrogen bonds: E:S.73, E:E.76 7PH.20: 19 residues within 4Å: Chain L: I.42, I.77, L.81, M.237, L.240, F.245 Chain M: L.269, K.272, T.273, I.276, L.277 Chain N: G.70, A.71, S.73, T.74, E.76, T.77, F.78 Ligands: 6PH.12 11 PLIP interactions: 2 interactions with chain L, 6 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: L:I.42, L:L.240, N:A.71, N:T.74, N:F.78, M:T.273, M:L.277 Hydrogen bonds: N:S.73, N:E.76, N:T.77 Salt bridges: M:K.272

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

FES.9: 10 residues within 4Å: Chain E: C.159, H.161, L.162, C.164, C.178, C.180, H.181, S.183, Y.185, P.195 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.159, E:H.181, E:S.183 FES.21: 10 residues within 4Å: Chain N: C.159, H.161, L.162, C.164, C.178, C.180, H.181, S.183, Y.185, P.195 3 PLIP interactions: 3 interactions with chain N, Metal complexes: N:C.159, N:H.181, N:S.183

2 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.10: 13 residues within 4Å: Chain A: D.428, S.453, M.455 Chain E: Y.57, G.64, S.68 Chain I: F.11, K.12, N.14, F.17, V.18, I.21 Ligands: 6PH.1 1 PLIP interactions: 1 interactions with chain E pi-Cation interactions: E:Y.57 PCF.22: 12 residues within 4Å: Chain J: D.428, S.453, M.455 Chain N: Y.57, G.64, S.68 Chain R: F.11, K.12, N.14, F.17, V.18 Ligands: 6PH.12 No protein-ligand interaction detected (PLIP)

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

9PE.11: 12 residues within 4Å: Chain C: N.7, Y.9, L.12, V.13, I.195 Chain L: T.112, N.115, V.116, I.119, I.195, M.196 Ligands: CN5.5 10 PLIP interactions: 6 interactions with chain L, 4 interactions with chain C Hydrophobic interactions: L:N.115, L:V.116, L:I.119, L:I.195, C:Y.9, C:L.12 Hydrogen bonds: L:T.112, L:N.115, C:N.7, C:N.7 9PE.17: 11 residues within 4Å: Chain C: V.111, T.112, N.115, I.119, M.196 Chain L: F.3, N.7, Y.9, L.12, V.13 Ligands: CN5.5 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain C Hydrophobic interactions: L:L.12, L:V.13, C:I.119 Hydrogen bonds: L:N.7, C:T.112, C:N.115

1 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)

CN3.18: 15 residues within 4Å: Chain L: N.27, Y.28, W.29, M.32, L.35, F.88, L.235, F.236 Chain M: Y.281, I.285, K.288, K.289 Chain P: H.85 Chain Q: R.51 Ligands: 8PE.16 13 PLIP interactions: 6 interactions with chain L, 3 interactions with chain Q, 3 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: L:L.35, L:F.88, L:L.235, L:F.236, M:I.285 Hydrogen bonds: L:Y.28, L:Y.28, Q:R.51 Salt bridges: Q:R.51, Q:R.51, M:K.288, M:K.289, P:H.85

1 x CU: COPPER (II) ION(Non-covalent)

CU.23: 4 residues within 4Å: Chain U: H.241, H.290, H.291 Ligands: HEA.25 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:H.241, U:H.290, U:H.291

2 x HEA: HEME-A(Non-covalent)

HEA.24: 30 residues within 4Å: Chain U: I.23, G.26, T.30, S.33, I.36, R.37, V.59, H.62, A.63, M.66, I.67, L.70, W.127, Y.371, V.374, F.377, H.378, L.381, S.382, I.386, L.389, F.390, I.417, F.425, R.438, R.439, S.458, A.461, L.465, F.468 25 PLIP interactions: 25 interactions with chain U, Hydrophobic interactions: U:I.23, U:A.63, U:I.67, U:L.70, U:Y.371, U:V.374, U:F.377, U:F.377, U:L.381, U:I.386, U:L.389, U:F.390, U:I.417, U:A.461, U:L.465, U:F.468, U:F.468 Hydrogen bonds: U:R.439 Salt bridges: U:R.438, U:R.438, U:R.439 pi-Stacking: U:H.62, U:H.378, U:F.425 Metal complexes: U:H.62 HEA.25: 28 residues within 4Å: Chain U: W.127, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, A.313, G.317, I.320, T.349, G.352, G.355, V.356, L.358, A.359, D.364, F.367, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain V: I.50 Ligands: CU.23 21 PLIP interactions: 21 interactions with chain U, Hydrophobic interactions: U:V.244, U:V.244, U:I.248, U:I.248, U:T.309, U:I.320, U:I.320, U:L.358, U:A.359, U:V.373, U:F.377, U:F.377, U:F.377, U:V.380, U:L.381, U:L.381 Hydrogen bonds: U:Y.245, U:H.291 Salt bridges: U:H.368, U:R.438 pi-Cation interactions: U:H.290

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.26: 7 residues within 4Å: Chain V: H.186, C.221, E.223, C.225, G.228, H.229, M.232 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:H.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rathore, S. et al., Cryo-EM structure of the yeast respiratory supercomplex. Nat. Struct. Mol. Biol. (2019)

Release Date

2019-01-02

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: 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: FO
Cytochrome b-c1 complex subunit 7: GP
Cytochrome b-c1 complex subunit 8: HQ
Cytochrome b-c1 complex subunit 9: IR
Cytochrome b-c1 complex subunit 10: ST
Cytochrome c oxidase subunit 1: U
Cytochrome c oxidase subunit 2: V
Cytochrome c oxidase subunit 3: W
Cytochrome c oxidase subunit 4, mitochondrial: X
Cytochrome c oxidase polypeptide 5A, mitochondrial: Y
Cytochrome c oxidase subunit 6, mitochondrial: Z
Cytochrome c oxidase subunit 7: 0
Cytochrome c oxidase polypeptide VIII, mitochondrial: 1
Cytochrome c oxidase subunit 7A: 2
Cytochrome c oxidase subunit 6B: 3
Cytochrome c oxidase subunit 6A, mitochondrial: 4
Unknown Cox subunit: 5

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

U
a

V
b

W
c

X
d

Y
e

Z
f

0
g

1
h

2
i

3
j

4
k

5
m

Membrane

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

Cytochrome b-c1 complex subunit 1, mitochondrial

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

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase polypeptide 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7

Cytochrome c oxidase polypeptide VIII, mitochondrial

Cytochrome c oxidase subunit 7A

Cytochrome c oxidase subunit 6B

Cytochrome c oxidase subunit 6A, mitochondrial

Unknown Cox subunit

Related Entries With Identical Sequence