SMTL ID : 8ec0.1

III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

15 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.1: 8 residues within 4Å: Chain A: S.450, S.453, M.454 Chain H: H.222, I.226, F.227 Ligands: PGT.2, PCF.6 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:I.226, H:F.227 Salt bridges: H:H.222 Hydrogen bonds: A:S.453 PEF.5: 15 residues within 4Å: Chain C: S.67, G.70, A.71, S.73, T.74, T.77 Chain D: D.33 Chain H: N.74, F.234, M.237 Chain J: K.272, T.273, I.276, L.277, L.280 10 PLIP interactions: 4 interactions with chain J, 3 interactions with chain H, 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: J:I.276, J:L.280, H:F.234, C:A.71, C:T.74 Hydrogen bonds: J:T.273, H:N.74, H:N.74, D:D.33 Salt bridges: J:K.272 PEF.7: 12 residues within 4Å: Chain G: L.37, Q.38, G.39, I.40, F.41, H.42 Chain U: K.89, G.90, S.93, K.97 Ligands: PGT.25, PCF.27 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain U Hydrophobic interactions: G:L.37, G:F.41, G:F.41 Hydrogen bonds: G:Q.38, G:H.42, U:S.93 Salt bridges: U:K.97 PEF.9: 12 residues within 4Å: Chain G: Q.55 Chain H: W.29, M.91, A.98, Y.102, Y.103, T.317, F.327, V.330, F.333 Ligands: PGT.8, PGT.20 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:W.29, H:W.29, H:A.98, H:V.330, H:F.333, H:F.333 Hydrogen bonds: H:Y.102, H:Y.103, G:Q.55 PEF.10: 5 residues within 4Å: Chain A: F.346, K.349, R.456 Chain H: F.3 Ligands: PEF.14 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:F.3 Salt bridges: A:R.456 PEF.14: 7 residues within 4Å: Chain 2: S.108, V.111, T.112, N.115 Chain H: N.7, Y.9 Ligands: PEF.10 4 PLIP interactions: 1 interactions with chain 2, 3 interactions with chain H Hydrogen bonds: 2:S.108, H:N.7, H:N.7 Hydrophobic interactions: H:Y.9 PEF.15: 7 residues within 4Å: Chain H: F.94, H.253, W.273, V.334, G.337, Q.338, A.341 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.94, H:W.273, H:V.334 PEF.23: 3 residues within 4Å: Chain I: I.456 Chain T: F.60 Ligands: PCF.26 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain T Hydrophobic interactions: I:I.456, T:F.60 PEF.24: 6 residues within 4Å: Chain G: F.46 Chain T: F.41, S.44, A.45 Chain U: L.87 Ligands: PCF.27 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.46 PEF.28: 11 residues within 4Å: Chain 2: H.222, I.226, D.229 Chain V: K.349, S.450, D.451, M.454 Chain X: A.71 Ligands: PGT.29, PCF.31, UQ6.37 5 PLIP interactions: 2 interactions with chain V, 1 interactions with chain X, 2 interactions with chain 2 Hydrogen bonds: V:K.349, V:K.349 Hydrophobic interactions: X:A.71 Salt bridges: 2:H.222, 2:H.222 PEF.32: 15 residues within 4Å: Chain 2: I.42, L.81, M.237, L.240, A.241, F.245 Chain 3: L.269, K.272, T.273, I.276, L.277 Chain X: G.70, S.73, T.74, T.77 12 PLIP interactions: 4 interactions with chain 3, 7 interactions with chain 2, 1 interactions with chain X Hydrophobic interactions: 3:T.273, 3:I.276, 3:L.277, 2:I.42, 2:L.81, 2:M.237, 2:L.240, 2:A.241, 2:F.245, 2:F.245 Salt bridges: 3:K.272 Hydrogen bonds: X:S.73 PEF.33: 17 residues within 4Å: Chain 1: R.51, Q.55 Chain 2: W.29, F.94, M.95, M.97, A.98, K.99, Y.102, Y.103, L.302, V.330, F.333, Y.359 Chain Z: E.82 Ligands: PEF.39, PGT.40 7 PLIP interactions: 6 interactions with chain 2, 1 interactions with chain Z Hydrophobic interactions: 2:W.29, 2:L.302, 2:F.333 Hydrogen bonds: 2:Y.102, 2:Y.102, 2:Y.103, Z:E.82 PEF.34: 5 residues within 4Å: Chain 2: F.3 Chain V: H.345, K.349 Ligands: PGT.29, PEF.38 3 PLIP interactions: 1 interactions with chain V, 2 interactions with chain 2 Hydrogen bonds: V:H.345 Hydrophobic interactions: 2:F.3, 2:F.3 PEF.38: 10 residues within 4Å: Chain 2: F.3, N.7, L.10 Chain H: S.108, T.112, N.115, I.119, M.193 Ligands: PGT.29, PEF.34 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:T.112, H:N.115, H:I.119 Hydrogen bonds: H:S.108 PEF.39: 6 residues within 4Å: Chain 2: M.91, H.253, W.273, F.333, Q.338 Ligands: PEF.33 3 PLIP interactions: 3 interactions with chain 2 Hydrophobic interactions: 2:W.273, 2:W.273, 2:F.333

7 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.2: 17 residues within 4Å: Chain A: D.341, H.345, L.443, R.447, D.451, M.454, M.455, R.456 Chain H: R.4, V.13, I.18, H.222, I.226, D.229 Ligands: PEF.1, PCF.6, UQ6.13 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: H:V.13, H:I.226 Hydrogen bonds: H:R.4, H:R.4, A:D.451 Salt bridges: H:R.4, H:R.4, A:R.447 PGT.4: 11 residues within 4Å: Chain C: K.44, E.45, K.51 Chain I: L.463, L.467 Chain U: F.94, G.98, G.102, F.105, L.109 Ligands: PGT.25 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain U, 2 interactions with chain C Hydrophobic interactions: I:L.467, U:L.109 Hydrogen bonds: C:K.44 Salt bridges: C:K.51 PGT.8: 12 residues within 4Å: Chain E: H.85 Chain G: S.48, R.51, F.52, V.59, L.60, A.63 Chain H: Y.28, W.29, M.95 Ligands: PEF.9, PGT.20 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:F.52, G:F.52, G:V.59, G:L.60, G:A.63, H:W.29 Salt bridges: G:R.51, G:R.51 PGT.20: 9 residues within 4Å: Chain E: H.85 Chain G: N.43, A.44 Chain H: Y.28 Chain J: K.288, K.289, K.296 Ligands: PGT.8, PEF.9 9 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G, 5 interactions with chain J Hydrophobic interactions: H:Y.28, G:A.44 Hydrogen bonds: H:Y.28, G:N.43, J:K.296 Salt bridges: J:K.288, J:K.288, J:K.289, J:K.296 PGT.25: 8 residues within 4Å: Chain G: K.35 Chain I: K.408 Chain U: F.94, K.97, L.104, F.105 Ligands: PGT.4, PEF.7 6 PLIP interactions: 5 interactions with chain U, 1 interactions with chain I Hydrophobic interactions: U:K.97, U:K.97, U:L.104, U:F.105 Salt bridges: U:K.97 Hydrogen bonds: I:K.408 PGT.29: 10 residues within 4Å: Chain 2: R.4, V.13, I.18 Chain V: H.345, R.447, D.451 Ligands: PEF.28, PCF.31, PEF.34, PEF.38 9 PLIP interactions: 3 interactions with chain V, 6 interactions with chain 2 Hydrogen bonds: V:H.345, V:D.451, 2:R.4, 2:R.4 Salt bridges: V:H.345, 2:R.4, 2:H.222 Hydrophobic interactions: 2:V.13, 2:I.18 PGT.40: 9 residues within 4Å: Chain 1: F.52, V.59 Chain 2: N.27, Y.28, W.29 Chain 3: K.288, K.296 Chain Z: H.85 Ligands: PEF.33 7 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain 1, 2 interactions with chain Z, 1 interactions with chain 3 Hydrophobic interactions: 2:Y.28, 2:W.29, 1:V.59 Hydrogen bonds: 2:N.27 Salt bridges: Z:H.85, Z:H.85, 3:K.289

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

FES.3: 9 residues within 4Å: Chain C: C.159, H.161, L.162, C.164, C.178, C.180, H.181, G.182, S.183 6 PLIP interactions: 6 interactions with chain C, Metal complexes: C:C.159, C:H.161, C:H.161, C:C.178, C:C.178, C:H.181 FES.30: 8 residues within 4Å: Chain X: C.159, H.161, L.162, C.164, C.178, H.181, S.183, Y.185 6 PLIP interactions: 6 interactions with chain X, Metal complexes: X:H.161, X:H.161, X:C.178, X:C.178, X:H.181, X:Y.185

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

PCF.6: 11 residues within 4Å: Chain A: W.427, S.453 Chain C: Y.57 Chain D: F.11, K.12, R.13, N.14, V.18, F.22 Ligands: PEF.1, PGT.2 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.18, D:F.22 Hydrogen bonds: D:N.14, C:Y.57 PCF.26: 7 residues within 4Å: Chain D: W.39, H.43 Chain U: R.114, M.115, G.118, Q.119 Ligands: PEF.23 2 PLIP interactions: 2 interactions with chain U Salt bridges: U:K.153, U:K.153 PCF.27: 2 residues within 4Å: Ligands: PEF.7, PEF.24 No protein-ligand interaction detected (PLIP) PCF.31: 15 residues within 4Å: Chain V: S.453, R.456 Chain X: Y.57, G.64, L.65, S.68 Chain Y: F.11, K.12, R.13, N.14, F.17, I.21, F.22 Ligands: PEF.28, PGT.29 3 PLIP interactions: 3 interactions with chain Y Hydrophobic interactions: Y:I.21, Y:F.22 pi-Cation interactions: Y:F.17

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

HEM.11: 14 residues within 4Å: Chain H: L.40, Q.43, G.47, A.51, Y.54, V.65, R.79, A.86, F.89, G.131, V.135, H.183, Y.184, Y.274 12 PLIP interactions: 12 interactions with chain H, Hydrophobic interactions: H:L.40, H:Q.43, H:A.51, H:Y.54, H:Y.54, H:F.89, H:V.135, H:Y.184 Salt bridges: H:R.79, H:R.79 pi-Stacking: H:H.183 Metal complexes: H:H.183 HEM.12: 21 residues within 4Å: Chain H: W.30, G.33, S.34, L.36, G.37, M.93, H.96, M.97, K.99, S.105, W.114, G.117, V.118, I.120, V.194, H.197, L.198, L.201, S.206, S.207 Ligands: UQ6.13 19 PLIP interactions: 19 interactions with chain H, Hydrophobic interactions: H:L.36, H:W.114, H:W.114, H:I.120, H:V.194, H:V.194, H:L.198, H:L.201 Hydrogen bonds: H:G.33, H:S.34, H:S.207 Salt bridges: H:H.96, H:K.99, H:K.99, H:R.110 pi-Stacking: H:H.96, H:H.96 Metal complexes: H:H.96, H:H.197 HEM.19: 14 residues within 4Å: Chain J: V.100, C.101, C.104, H.105, N.169, A.172, L.173, P.174, P.175, L.177, I.180, R.184, I.223, M.225 5 PLIP interactions: 5 interactions with chain J, Hydrophobic interactions: J:V.100, J:L.177, J:I.223 Salt bridges: J:R.184 Metal complexes: J:H.105 HEM.35: 18 residues within 4Å: Chain 2: Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, H.82, A.86, F.90, A.128, G.131, Y.132, C.134, V.135, H.183, Y.184, N.256 12 PLIP interactions: 12 interactions with chain 2, Hydrophobic interactions: 2:Q.43, 2:A.51, 2:F.90, 2:A.128, 2:Y.132, 2:V.135, 2:Y.184 Hydrogen bonds: 2:Y.54, 2:N.256 Salt bridges: 2:H.183 Metal complexes: 2:H.82, 2:H.183 HEM.36: 20 residues within 4Å: Chain 2: W.30, L.36, F.89, 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: UQ6.37 12 PLIP interactions: 12 interactions with chain 2, Hydrophobic interactions: 2:L.36, 2:F.89, 2:L.113, 2:I.120, 2:V.194, 2:L.198, 2:L.201 Hydrogen bonds: 2:S.105, 2:S.206, 2:S.207 Salt bridges: 2:K.99 Metal complexes: 2:H.197 HEM.41: 12 residues within 4Å: Chain 3: C.101, C.104, H.105, A.172, L.173, P.174, P.175, L.177, I.180, I.191, L.194, M.225 7 PLIP interactions: 6 interactions with chain 3, 1 interactions with chain C, Hydrophobic interactions: 3:P.174, 3:P.175, 3:L.177, 3:I.191 pi-Stacking: 3:H.105 Metal complexes: 3:H.105 Salt bridges: C:K.105

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)

UQ6.13: 9 residues within 4Å: Chain 2: L.185 Chain H: Q.22, S.34, V.41, L.201, M.221, D.229 Ligands: PGT.2, HEM.12 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain 2 Hydrophobic interactions: H:V.41, 2:L.185 Hydrogen bonds: H:Q.22, H:S.34, H:S.34 UQ6.37: 12 residues within 4Å: Chain 2: Y.16, I.17, Q.22, S.34, L.38, V.41, I.195, L.201, H.202, M.221 Ligands: PEF.28, HEM.36 5 PLIP interactions: 5 interactions with chain 2 Hydrophobic interactions: 2:I.17, 2:L.38, 2:I.195 Hydrogen bonds: 2:Y.16, 2:Q.22

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

CU.16: 3 residues within 4Å: Chain I: H.241, V.287, H.290 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.241, I:H.241, I:V.287, I:H.290

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

HEA.17: 25 residues within 4Å: Chain I: F.19, I.23, G.26, M.27, T.30, R.37, L.40, F.55, V.59, H.62, A.63, M.66, I.67, G.126, W.127, F.377, H.378, L.381, S.382, I.386, L.389, F.390, Y.393, R.439, L.465 21 PLIP interactions: 21 interactions with chain I, Hydrophobic interactions: I:F.19, I:I.23, I:V.59, I:A.63, I:I.67, I:I.67, I:F.377, I:L.381, I:I.386, I:I.386, I:L.389, I:F.390, I:Y.393, I:L.465 Hydrogen bonds: I:W.127, I:W.127, I:S.382 pi-Stacking: I:H.62, I:H.378, I:H.378 Metal complexes: I:H.62 HEA.18: 25 residues within 4Å: Chain I: W.127, W.237, V.244, I.248, H.290, H.291, A.313, T.316, G.317, F.348, G.352, L.353, G.355, V.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381 Chain N: I.50, P.89 21 PLIP interactions: 2 interactions with chain N, 19 interactions with chain I, Hydrophobic interactions: N:I.50, N:P.89, I:W.237, I:V.244, I:I.248, I:T.316, I:F.348, I:F.348, I:V.356, I:L.358, I:L.358, I:L.358, I:A.359, I:V.373, I:F.377, I:V.380, I:V.380, I:L.381 Salt bridges: I:H.291 pi-Stacking: I:H.290 Metal complexes: I:H.376

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

CUA.21: 5 residues within 4Å: Chain N: H.186, C.221, C.225, M.232 Ligands: CUA.22 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.186, N:C.221, N:C.225 CUA.22: 6 residues within 4Å: Chain N: C.221, E.223, C.225, H.229, M.232 Ligands: CUA.21 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.221, N:E.223, N:C.225, N:H.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hryc, C.F. et al., Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex. Nat Commun (2023)

Release Date

2023-05-24

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AV
Cytochrome b-c1 complex subunit 2, mitochondrial: BW
Cytochrome b-c1 complex subunit Rieske, mitochondrial: CX
Cytochrome b-c1 complex subunit 9, mitochondrial: DY
Cytochrome b-c1 complex subunit 7, mitochondrial: EZ
Cytochrome b-c1 complex subunit 6, mitochondrial: F0
Cytochrome b-c1 complex subunit 8, mitochondrial: G1
Cytochrome b: H2
Cytochrome c oxidase subunit 1: I
Cytochrome c1, heme protein, mitochondrial: J3
Cytochrome c oxidase subunit 8, mitochondrial: K
Cytochrome c oxidase subunit 7, mitochondrial: L
Cytochrome c oxidase subunit 3: M
Cytochrome c oxidase subunit 2: N
Cytochrome c oxidase subunit 6, mitochondrial: O
Cytochrome c oxidase subunit 9, mitochondrial: P
Cytochrome c oxidase subunit 13, mitochondrial: Q
Cytochrome c oxidase subunit 4, mitochondrial: R
Cytochrome c oxidase subunit 12, mitochondrial: S
Cytochrome c oxidase subunit 26, mitochondrial: T
Cytochrome c oxidase subunit 5A, mitochondrial: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

V
a

B
B

W
b

C
C

X
c

D
E

Y
e

E
F

Z
f

F
G

0
g

G
H

1
h

H
J

2
j

I
K

J
L

3
l

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
W

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9, mitochondrial

Cytochrome b-c1 complex subunit 7, mitochondrial

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 8, mitochondrial

Cytochrome b

Cytochrome c oxidase subunit 1

Cytochrome c1, heme protein, mitochondrial

Cytochrome c oxidase subunit 8, mitochondrial

Cytochrome c oxidase subunit 7, mitochondrial

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

Cytochrome c oxidase subunit 13, mitochondrial

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase subunit 12, mitochondrial

Cytochrome c oxidase subunit 26, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

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