SMTL ID : 7o3e.1

Murine supercomplex CIII2CIV in the intermediate locked conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 22 residues within 4Å: Chain C: Q.44, I.45, G.48, L.51, Y.55, R.80, H.83, A.84, A.87, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, N.255, Y.273 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:Y.55, C:A.87, C:V.123, C:A.127, C:L.133, C:F.179, C:F.183 Hydrogen bonds: C:N.255 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.2: 18 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, L.119, L.120, H.196, L.197, L.200, S.205, N.206 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:W.113, C:W.113, C:L.119, C:L.120, C:L.197 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Stacking: C:H.97 Metal complexes: C:H.97, C:H.196 HEM.12: 21 residues within 4Å: Chain J: Q.44, G.48, L.51, R.80, H.83, A.84, A.87, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, E.271, Y.273 12 PLIP interactions: 12 interactions with chain J, Hydrophobic interactions: J:Q.44, J:L.51, J:L.51, J:A.127, J:L.133, J:F.179, J:F.183, J:F.187 Salt bridges: J:R.80, J:R.80 Metal complexes: J:H.83, J:H.182 HEM.13: 17 residues within 4Å: Chain J: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, L.119, H.196, L.197, L.200, S.205, N.206 15 PLIP interactions: 15 interactions with chain J, Hydrophobic interactions: J:L.37, J:L.37, J:W.113, J:W.113, J:L.119, J:L.197, J:L.200 Hydrogen bonds: J:S.106, J:N.206, J:N.206 Salt bridges: J:R.100, J:R.100 pi-Cation interactions: J:R.100 Metal complexes: J:H.97, J:H.196

13 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 17 residues within 4Å: Chain C: W.30, F.95, L.96, V.98, G.99, Y.103, Y.104, L.301, M.316, Q.322, Y.325, W.326, L.332, Y.358 Chain F: R.44, V.48 Ligands: CDL.4 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:F.95, C:L.96, C:V.98, C:L.301, C:W.326, C:W.326, C:L.332 Hydrogen bonds: C:Y.104, C:Q.322 Salt bridges: F:R.44 3PE.7: 8 residues within 4Å: Chain 0: N.17, W.19 Chain E: K.11, W.12, G.15, F.16, W.19 Ligands: 3PE.8 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain 0 Hydrophobic interactions: E:W.12, E:F.16, E:F.16 Hydrogen bonds: 0:N.17, 0:W.19 3PE.8: 12 residues within 4Å: Chain 0: R.20 Chain C: P.319, I.320, I.323 Chain E: W.19, Y.20, A.23 Chain F: R.42, E.43, L.46, R.47 Ligands: 3PE.7 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F, 1 interactions with chain 0 Hydrophobic interactions: C:I.323, F:L.46, 0:R.20 Salt bridges: F:R.47 3PE.10: 7 residues within 4Å: Chain H: S.439, F.442, L.444 Chain J: H.221, I.226 Ligands: PC1.9, CDL.11 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain J Hydrophobic interactions: H:L.444, J:I.226 Hydrogen bonds: H:S.439, H:S.439 Salt bridges: J:H.221, J:H.221 3PE.14: 15 residues within 4Å: Chain J: W.30, F.95, V.98, G.99, Y.103, Y.104, L.301, M.316, Q.322, Y.325, W.326, L.332 Chain M: R.44, V.48 Ligands: CDL.15 12 PLIP interactions: 10 interactions with chain J, 2 interactions with chain M Hydrophobic interactions: J:W.30, J:W.30, J:W.30, J:V.98, J:Y.103, J:L.301, J:Y.325, M:V.48 Hydrogen bonds: J:Y.104, J:Y.104, J:Q.322 Salt bridges: M:R.44 3PE.16: 12 residues within 4Å: Chain J: P.319, I.320, I.323, I.327, L.353, A.354 Chain L: W.19 Chain M: R.42, L.46, R.47, V.54, V.55 9 PLIP interactions: 4 interactions with chain M, 5 interactions with chain J Hydrophobic interactions: M:V.54, M:V.54, M:V.55, J:I.323, J:I.327, J:I.327, J:I.327, J:L.353 Salt bridges: M:R.47 3PE.22: 12 residues within 4Å: Chain Q: F.94, R.96, M.97, M.100, L.159 Chain S: V.11, W.57, W.58, V.61, L.79, F.86 Ligands: 3PE.27 5 PLIP interactions: 2 interactions with chain S, 3 interactions with chain Q Hydrophobic interactions: S:L.79, S:F.86, Q:L.159 Hydrogen bonds: Q:M.97 Salt bridges: Q:R.96 3PE.24: 11 residues within 4Å: Chain Q: F.426, H.429, F.430, L.433 Chain R: L.7, G.8, L.28, F.32 Chain Y: Y.37, V.41, R.45 5 PLIP interactions: 2 interactions with chain R, 2 interactions with chain Q, 1 interactions with chain Y Hydrophobic interactions: R:F.32, Q:F.426, Q:F.426 Hydrogen bonds: R:G.8 Salt bridges: Y:R.45 3PE.26: 6 residues within 4Å: Chain R: H.26, M.29, M.75 Chain Y: A.35, K.38, F.39 3 PLIP interactions: 1 interactions with chain R, 2 interactions with chain Y Hydrogen bonds: R:H.26 Salt bridges: Y:K.38, Y:K.38 3PE.27: 21 residues within 4Å: Chain S: I.51, W.58, V.61, I.62, G.65, T.66, H.71, L.79, M.83, F.86, I.210, T.213, F.214, V.217, R.221, H.226, F.227, H.231, F.233, G.234 Ligands: 3PE.22 21 PLIP interactions: 21 interactions with chain S Hydrophobic interactions: S:I.51, S:W.58, S:W.58, S:W.58, S:W.58, S:W.58, S:W.58, S:I.62, S:F.86, S:I.210, S:I.210, S:F.214, S:F.214, S:V.217, S:F.233 Hydrogen bonds: S:H.226, S:F.233, S:G.234 Salt bridges: S:R.221, S:R.221, S:H.231 3PE.28: 12 residues within 4Å: Chain Q: W.334, L.339, L.342, A.415, F.418, V.419 Chain T: N.72, R.73, T.75, E.77, W.78, V.81 9 PLIP interactions: 6 interactions with chain Q, 3 interactions with chain T Hydrophobic interactions: Q:L.339, Q:L.342, Q:A.415, Q:F.418, Q:V.419, T:W.78, T:V.81 Salt bridges: Q:K.411 Hydrogen bonds: T:R.73 3PE.30: 16 residues within 4Å: Chain Q: L.215 Chain S: Y.181, F.182, T.184, F.186, S.187, I.188, F.198, M.199, G.202, F.203 Chain W: W.62, T.68, L.69, F.70, N.76 10 PLIP interactions: 2 interactions with chain S, 7 interactions with chain W, 1 interactions with chain Q Hydrophobic interactions: S:F.203, W:W.62, W:L.69, Q:L.215 Hydrogen bonds: S:I.188, W:T.68, W:L.69, W:F.70, W:N.76, W:N.76 3PE.31: 10 residues within 4Å: Chain 1: A.12, Q.15, I.19 Chain Q: D.406, T.408, W.409 Chain T: M.84, F.87 Chain Z: F.9, H.10 4 PLIP interactions: 1 interactions with chain T, 3 interactions with chain 1 Hydrophobic interactions: T:F.87, 1:A.12, 1:Q.15, 1:I.19

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 11 residues within 4Å: Chain C: S.28, S.29, W.30, F.33, Y.104 Chain E: H.72 Chain F: V.37, R.40, T.41, R.44 Ligands: 3PE.3 11 PLIP interactions: 7 interactions with chain C, 1 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: C:W.30, C:F.33 Hydrogen bonds: C:S.28, C:S.28, C:S.29, C:S.29, C:Y.104 Salt bridges: E:H.72, F:R.40, F:R.40, F:R.40 CDL.5: 14 residues within 4Å: Chain C: S.29, N.32, F.33, I.92, K.227, L.230, I.234, I.238 Chain D: Y.220, K.223, R.224 Chain F: I.34, V.37, R.40 10 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: C:F.33, C:I.92, C:I.234, D:Y.220, D:Y.220 Salt bridges: C:K.227, D:K.223, F:R.40 Hydrogen bonds: D:Y.220, D:R.224 CDL.11: 10 residues within 4Å: Chain H: F.336, W.443, L.444, R.445 Chain J: N.3, R.5, F.18, I.19, H.221 Ligands: 3PE.10 10 PLIP interactions: 5 interactions with chain H, 5 interactions with chain J Hydrophobic interactions: H:R.445, J:F.18 Hydrogen bonds: H:L.444, J:N.3, J:N.3 Salt bridges: H:R.436, H:R.445, H:R.445, J:R.5, J:H.221 CDL.15: 10 residues within 4Å: Chain J: S.29, W.30, F.33 Chain L: H.72 Chain M: V.37, R.40, T.41, R.44 Ligands: 3PE.14, CDL.33 10 PLIP interactions: 4 interactions with chain J, 5 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: J:W.30, J:F.33, M:V.37, M:T.41 Hydrogen bonds: J:S.29, J:S.29, M:R.40 Salt bridges: M:R.40, M:R.40, L:H.72 CDL.33: 17 residues within 4Å: Chain 4: Y.220, K.223, R.224 Chain J: S.29, F.33, K.227, L.230, I.234, I.238 Chain L: H.72 Chain M: Y.29, F.30, G.33, I.34, V.37, R.40 Ligands: CDL.15 12 PLIP interactions: 4 interactions with chain J, 6 interactions with chain 4, 2 interactions with chain M Hydrophobic interactions: J:F.33, J:I.234, J:I.238, 4:Y.220 Salt bridges: J:K.227, 4:K.223, 4:R.224, 4:R.224, 4:K.231, M:R.40 Hydrogen bonds: 4:Y.220, M:R.40

2 x HEC: HEME C(Covalent)

HEC.6: 16 residues within 4Å: Chain D: C.37, C.40, H.41, N.105, A.108, L.109, P.110, R.120, Y.126, L.130, F.153, I.158, G.159, M.160, P.163, L.190 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:A.108, D:L.130, D:M.160, D:P.163, D:L.190 Hydrogen bonds: D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.34: 19 residues within 4Å: Chain 4: V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160 12 PLIP interactions: 12 interactions with chain 4, Hydrophobic interactions: 4:N.105, 4:A.108, 4:P.110, 4:I.116, 4:L.130, 4:L.131, 4:I.158 Hydrogen bonds: 4:Y.126, 4:G.159, 4:M.160 Salt bridges: 4:R.120 Metal complexes: 4:H.41

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.9: 6 residues within 4Å: Chain 4: M.222, K.226 Chain H: D.417, F.442, L.444 Ligands: 3PE.10 2 PLIP interactions: 1 interactions with chain 4, 1 interactions with chain H Salt bridges: 4:K.226, H:D.417 PC1.21: 10 residues within 4Å: Chain Q: H.233, L.297, D.300, T.301, A.303, Y.304, S.307, I.311 Chain R: L.81, Y.85 6 PLIP interactions: 5 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: Q:D.300, Q:A.303, Q:Y.304, Q:I.311, R:L.81 Hydrogen bonds: Q:T.301

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

CU.17: 4 residues within 4Å: Chain Q: H.240, H.290, H.291 Ligands: HEA.20 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:H.240, Q:H.290, Q:H.291

1 x NA: SODIUM ION(Non-functional Binders)

NA.18: 4 residues within 4Å: Chain Q: E.40, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:E.40, Q:D.442

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

HEA.19: 32 residues within 4Å: Chain Q: A.24, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, M.73, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, M.390, F.393, T.424, F.425, Q.428, R.439, Y.440, V.465, M.468 Ligands: TGL.32 34 PLIP interactions: 34 interactions with chain Q, Hydrophobic interactions: Q:A.24, Q:I.37, Q:R.38, Q:V.58, Q:V.58, Q:A.62, Q:M.65, Q:I.66, Q:V.70, Q:F.377, Q:F.377, Q:L.381, Q:V.386, Q:V.386, Q:F.393, Q:F.393, Q:T.424, Q:F.425, Q:V.465 Hydrogen bonds: Q:R.38, Q:W.126, Q:Y.371, Q:Q.428, Q:R.439, Q:Y.440 Salt bridges: Q:R.438, Q:R.439 pi-Stacking: Q:H.61, Q:H.61, Q:H.378, Q:H.378, Q:F.425 Metal complexes: Q:H.61, Q:H.378 HEA.20: 32 residues within 4Å: Chain Q: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.316, G.317, V.320, F.348, G.352, L.353, G.355, I.356, L.358, S.359, D.364, L.367, H.368, D.369, V.373, H.376, F.377, V.380, L.381, R.438 Chain R: I.34, P.69, I.72, L.73 Ligands: CU.17 32 PLIP interactions: 28 interactions with chain Q, 4 interactions with chain R, Hydrophobic interactions: Q:W.126, Q:W.236, Q:V.243, Q:V.243, Q:Y.244, Q:I.247, Q:T.316, Q:F.348, Q:F.348, Q:L.353, Q:I.356, Q:V.373, Q:F.377, Q:F.377, Q:V.380, Q:L.381, Q:L.381, R:I.34, R:P.69, R:I.72, R:L.73 Hydrogen bonds: Q:W.126, Q:Y.244, Q:L.367, Q:D.369 Salt bridges: Q:H.368, Q:R.438 pi-Stacking: Q:H.240, Q:H.376, Q:H.376 pi-Cation interactions: Q:H.240 Metal complexes: Q:H.376

1 x MG: MAGNESIUM ION(Non-covalent)

MG.23: 4 residues within 4Å: Chain Q: T.294, H.368 Chain R: D.173, E.198 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.198

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

CUA.25: 6 residues within 4Å: Chain R: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain R Metal complexes: R:H.161, R:C.196, R:C.196, R:E.198, R:C.200, R:C.200, R:H.204

1 x ZN: ZINC ION(Non-covalent)

ZN.29: 5 residues within 4Å: Chain V: C.61, C.63, C.83, N.85, C.86 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.61, V:C.63, V:C.83, V:C.86

1 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.32: 20 residues within 4Å: Chain 0: P.12, F.13, R.20, M.24, M.25, Y.28, F.29 Chain F: R.42 Chain Q: T.17, L.18, L.20, L.21, F.22, W.25, F.109, L.110, F.393, F.400, I.472 Ligands: HEA.19 20 PLIP interactions: 14 interactions with chain Q, 6 interactions with chain 0 Hydrophobic interactions: Q:T.17, Q:L.20, Q:L.20, Q:F.22, Q:F.22, Q:W.25, Q:W.25, Q:F.109, Q:L.110, Q:L.110, Q:F.393, Q:F.400, Q:I.472, Q:I.472, 0:F.13, 0:F.13, 0:F.13, 0:Y.28, 0:Y.28, 0:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vercellino, I. et al., Structure and assembly of the mammalian mitochondrial supercomplex CIII 2 CIV. Nature (2021)

Release Date

2021-10-13

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AH
Cytochrome b-c1 complex subunit 2, mitochondrial: BI
Cytochrome b: CJ
Cytochrome c1, heme protein, mitochondrial: D4
Cytochrome b-c1 complex subunit 7: EL
Cytochrome b-c1 complex subunit 8: FM
Cytochrome b-c1 complex subunit 6, mitochondrial: GN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: K
Cytochrome b-c1 complex subunit 9: O
Cox7a2l protein: P
Cytochrome c oxidase subunit 1: Q
Cytochrome c oxidase subunit 2: R
Cytochrome c oxidase subunit 3: S
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: T
Cytochrome c oxidase subunit 5A, mitochondrial: U
Cytochrome c oxidase subunit 5B, mitochondrial: V
Cytochrome c oxidase subunit 6A2, mitochondrial: W
Cytochrome c oxidase subunit 6B1: X
Cytochrome c oxidase subunit 6C: Y
Cytochrome c oxidase subunit 7B, mitochondrial: Z
Cytochrome c oxidase subunit 7C, mitochondrial: 0
Cytochrome c oxidase subunit 8B, mitochondrial: 1
Cytochrome b-c1 complex subunit 9: 23

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
L

B
B

I
M

C
C

J
N

D
D

4
O

E
F

L
Q

F
G

M
R

G
H

N
S

K
P

O
T

P
I

Q
a

R
b

S
c

T
d

U
e

V
f

W
g

X
h

Y
i

Z
k

0
l

1
m

2
J

3
U

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

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cox7a2l protein

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

Cytochrome b-c1 complex subunit 9

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