SMTL ID : 7o37.1

Murine supercomplex CIII2CIV in the assembled locked conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

3PE.1: 8 residues within 4Å: Chain A: S.439, F.442, L.444 Chain C: H.221, T.225, I.229 Ligands: CDL.2, PC1.10 Ligand excluded by PLIP 3PE.5: 19 residues within 4Å: Chain C: W.30, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, L.301, M.316, Q.322, Y.325, W.326, L.332, Y.358 Chain G: R.44, V.48 Ligands: CDL.12 Ligand excluded by PLIP 3PE.7: 17 residues within 4Å: Chain C: V.43, M.82, L.233, F.236, M.240 Chain D: H.200, M.204, K.207, M.208, M.211, M.212 Chain E: Y.49, A.50, N.53, V.54, Q.57 Chain I: D.36 Ligand excluded by PLIP 3PE.11: 11 residues within 4Å: Chain 6: N.17, W.19, R.20, M.24 Chain F: K.11, W.12, G.15, W.19, N.22 Chain G: L.46 Ligands: 3PE.13 Ligand excluded by PLIP 3PE.13: 9 residues within 4Å: Chain C: P.319, I.320, I.323 Chain F: W.19 Chain G: R.42, I.45, L.46, R.47 Ligands: 3PE.11 Ligand excluded by PLIP 3PE.17: 7 residues within 4Å: Chain K: S.439, F.442, L.444 Chain M: H.221, T.225 Ligands: CDL.18, PC1.28 Ligand excluded by PLIP 3PE.21: 16 residues within 4Å: Chain M: W.30, F.95, L.96, V.98, G.99, Y.103, Y.104, L.301, M.316, Q.322, Y.325, W.326, V.329, L.332 Chain Q: R.44 Ligands: CDL.26 Ligand excluded by PLIP 3PE.23: 11 residues within 4Å: Chain M: M.240 Chain N: H.200, M.204, K.207, M.208, M.211 Chain O: Y.49, A.50, N.53, Q.57 Chain S: D.36 Ligand excluded by PLIP 3PE.27: 14 residues within 4Å: Chain M: P.319, I.320, I.323, I.327, L.353, A.354, S.357 Chain P: W.19, A.23 Chain Q: R.42, E.43, L.46, R.47, V.54 Ligand excluded by PLIP 3PE.33: 13 residues within 4Å: Chain W: W.334, L.339, L.342, A.415, F.418, V.419 Chain Z: N.72, R.73, G.74, T.75, E.77, W.78, V.81 Ligand excluded by PLIP 3PE.35: 13 residues within 4Å: Chain W: F.94, R.96, M.97, M.100, L.159 Chain Y: V.11, W.57, W.58, V.61, E.64, L.79, F.86 Ligands: 3PE.40 Ligand excluded by PLIP 3PE.37: 11 residues within 4Å: Chain 4: Y.37, R.45 Chain W: F.426, H.429, F.430, L.433 Chain X: L.7, G.8, L.28, V.31, F.32 Ligand excluded by PLIP 3PE.39: 7 residues within 4Å: Chain 4: G.32, A.35, F.39 Chain X: M.29, I.30, L.33, M.75 Ligand excluded by PLIP 3PE.40: 19 residues within 4Å: Chain Y: W.58, V.61, I.62, T.66, H.71, L.79, M.83, F.86, I.210, T.213, F.214, V.217, R.221, H.226, H.231, H.232, F.233, G.234 Ligands: 3PE.35 Ligand excluded by PLIP 3PE.42: 15 residues within 4Å: Chain 2: W.62, T.68, L.69, F.70, N.76 Chain W: L.215 Chain Y: Y.181, F.182, T.184, F.186, S.187, I.188, F.198, M.199, G.202 Ligand excluded by PLIP 3PE.43: 9 residues within 4Å: Chain 5: F.9, I.17 Chain 7: A.12, Q.15 Chain W: D.406, W.409 Chain Z: T.80, M.84, F.87 Ligand excluded by PLIP

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 10 residues within 4Å: Chain A: F.336, W.443, L.444, R.445 Chain C: R.5, I.19, H.221, T.225 Chain J: W.24 Ligands: 3PE.1 10 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: C:I.19, C:T.225, A:L.444, J:W.24 Salt bridges: C:R.5, C:H.221, A:R.445, A:R.445 Hydrogen bonds: A:L.444, A:R.445 CDL.6: 22 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, I.92, G.231, I.234 Chain D: L.216, P.217, Y.220, K.223, R.224, K.231 Chain G: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.12 13 PLIP interactions: 4 interactions with chain G, 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: G:F.30, G:I.34, C:F.33, C:L.36, C:I.92, C:I.234, D:L.216, D:P.217, D:Y.220 Hydrogen bonds: G:N.36, G:R.40, D:Y.220 Salt bridges: D:K.223 CDL.12: 11 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Chain F: H.72 Chain G: V.37, R.40, T.41, R.44 Ligands: 3PE.5, CDL.6 9 PLIP interactions: 4 interactions with chain G, 4 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:V.37, C:W.30, C:F.33 Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72 Hydrogen bonds: C:S.29, C:S.29 CDL.18: 12 residues within 4Å: Chain K: F.336, W.443, L.444, R.445 Chain M: N.3, R.5, F.18, I.19, H.221, T.225 Chain T: W.24 Ligands: 3PE.17 9 PLIP interactions: 4 interactions with chain K, 4 interactions with chain M, 1 interactions with chain T Hydrophobic interactions: K:R.445, M:F.18, M:I.19, T:W.24 Hydrogen bonds: K:L.444, K:R.445 Salt bridges: K:R.445, M:R.5, M:H.221 CDL.22: 25 residues within 4Å: Chain M: S.29, N.32, F.33, M.89, I.92, K.227, L.230, G.231, I.234, I.238 Chain N: L.216, Y.220, K.223, R.224, K.231 Chain P: H.72 Chain Q: Y.29, F.30, K.32, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.26 19 PLIP interactions: 4 interactions with chain Q, 7 interactions with chain M, 8 interactions with chain N Hydrophobic interactions: Q:I.34, M:N.32, M:F.33, M:F.33, M:I.92, M:I.234, M:I.238, N:L.216, N:Y.220, N:Y.220 Hydrogen bonds: Q:K.32, Q:N.36, M:N.32, N:Y.220 Salt bridges: Q:R.40, N:K.223, N:R.224, N:R.224, N:K.231 CDL.26: 9 residues within 4Å: Chain M: S.29, W.30, F.33 Chain P: H.72 Chain Q: R.40, T.41, R.44 Ligands: 3PE.21, CDL.22 8 PLIP interactions: 4 interactions with chain M, 3 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:F.33 Hydrogen bonds: M:S.29, M:S.29, M:W.30 Salt bridges: Q:R.40, Q:R.40, Q:R.40, P:H.72

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

HEM.3: 20 residues within 4Å: Chain C: Q.44, 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, Y.273 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Q.44, C:L.51, C:L.51, C:Y.55, C:A.84, C:T.126, C:A.127, C:L.133, C:F.179, C:F.183, C:P.186 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.182 pi-Cation interactions: C:H.182 Metal complexes: C:H.83, C:H.182 HEM.4: 18 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, L.119, H.196, L.197, L.200, S.205, N.206 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:T.112, C:W.113, C:L.119, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.19: 20 residues within 4Å: Chain M: Q.44, I.45, G.48, L.51, V.66, R.80, H.83, A.84, A.87, F.90, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 16 PLIP interactions: 16 interactions with chain M, Hydrophobic interactions: M:Q.44, M:Q.44, M:I.45, M:L.51, M:L.51, M:A.84, M:F.90, M:L.133, M:F.179, M:F.183, M:P.186, M:F.187 Salt bridges: M:R.80, M:R.80 Metal complexes: M:H.83, M:H.182 HEM.20: 18 residues within 4Å: Chain M: 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 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:L.94, M:W.113, M:L.120, M:L.197, M:L.200 Hydrogen bonds: M:G.34, M:S.106, M:N.206 Salt bridges: M:H.97, M:R.100, M:R.100 Metal complexes: M:H.97, M:H.196

2 x HEC: HEME C(Covalent)

HEC.8: 19 residues within 4Å: Chain D: V.36, C.37, 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, G.159, M.160, P.163, I.164 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:V.36, D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:L.130, D:L.131, D:F.153, D:M.160, D:P.163, D:I.164 Hydrogen bonds: D:Y.126, D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.24: 21 residues within 4Å: Chain N: 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, P.163, I.164 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:V.36, N:N.105, N:P.110, N:P.111, N:I.116, N:L.130, N:L.131, N:P.163, N:P.163, N:I.164 Hydrogen bonds: N:Y.126, N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41 Metal complexes: N:H.41

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

FES.9: 8 residues within 4Å: Chain E: C.139, H.141, L.142, C.158, C.160, H.161, S.163, P.175 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.139, E:C.158 FES.25: 8 residues within 4Å: Chain O: C.139, T.140, H.141, L.142, C.158, H.161, S.163, A.176 5 PLIP interactions: 5 interactions with chain O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161, O:H.161

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

PC1.10: 16 residues within 4Å: Chain A: D.417, F.442 Chain C: I.229 Chain D: M.222 Chain E: Y.37, T.40, T.43, T.44, V.47 Chain I: F.14, T.17, F.20, A.21, I.24 Chain J: W.34 Ligands: 3PE.1 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain E, 1 interactions with chain A, 1 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: I:A.21, I:I.24, E:T.43, E:V.47, J:W.34, C:I.229 pi-Cation interactions: I:F.20, E:Y.37 Hydrogen bonds: E:T.40 Salt bridges: A:D.417 PC1.14: 10 residues within 4Å: Chain G: F.26, S.28, Y.29, F.30, S.31, I.34, P.35 Chain V: R.87, M.90 Chain W: I.3 11 PLIP interactions: 7 interactions with chain G, 2 interactions with chain V, 2 interactions with chain W Hydrophobic interactions: G:F.30, G:I.34, W:I.3, W:I.3 Hydrogen bonds: G:Y.29, G:F.30, G:S.31 pi-Cation interactions: G:F.26, G:Y.29 Salt bridges: V:R.87, V:R.87 PC1.16: 9 residues within 4Å: Chain 7: W.32, S.39, Y.40 Chain C: I.349, L.353 Chain G: L.57, I.58, W.61, Q.64 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain 7 Hydrophobic interactions: G:L.57, G:L.57, 7:Y.40 PC1.28: 11 residues within 4Å: Chain K: D.417, F.442, L.444 Chain N: M.222 Chain O: Y.37, T.40, T.44 Chain S: F.14, T.17, F.20 Ligands: 3PE.17 6 PLIP interactions: 3 interactions with chain S, 2 interactions with chain K, 1 interactions with chain O Hydrophobic interactions: S:T.17, S:F.20, K:L.444 pi-Cation interactions: S:F.20, O:Y.37 Salt bridges: K:D.417 PC1.34: 8 residues within 4Å: Chain W: H.233, D.300, T.301, A.303, Y.304, S.307 Chain X: L.81, Y.85 5 PLIP interactions: 3 interactions with chain W, 2 interactions with chain X Hydrophobic interactions: W:A.303, W:Y.304, W:Y.304, X:L.81, X:Y.85

1 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.15: 17 residues within 4Å: Chain 6: P.12, F.13, M.24, M.25, Y.28, F.29 Chain G: R.42 Chain W: T.17, L.21, F.22, W.25, F.109, L.110, F.393, F.400, I.472 Ligands: HEA.31 15 PLIP interactions: 8 interactions with chain W, 7 interactions with chain 6 Hydrophobic interactions: W:T.17, W:F.22, W:W.25, W:F.109, W:L.110, W:F.393, W:F.400, W:I.472, 6:F.13, 6:F.13, 6:F.13, 6:F.13, 6:Y.28, 6:Y.28, 6:F.29

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

CU.29: 3 residues within 4Å: Chain W: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:H.240, W:H.290, W:H.291

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

NA.30: 3 residues within 4Å: Chain W: E.40, G.45, S.441 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:E.40, W:D.442

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

HEA.31: 34 residues within 4Å: Chain W: 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, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 Ligands: TGL.15 33 PLIP interactions: 33 interactions with chain W, Hydrophobic interactions: W:A.24, W:I.37, W:R.38, W:V.58, W:V.58, W:A.62, W:M.65, W:I.66, W:V.70, W:F.377, W:F.377, W:V.386, W:V.386, W:F.393, W:F.393, W:T.424, W:F.425 Hydrogen bonds: W:R.38, W:W.126, W:Y.371, W:Q.428, W:R.439, W:Y.440 Salt bridges: W:R.438, W:R.439 pi-Stacking: W:H.61, W:H.61, W:H.378, W:H.378, W:H.378, W:F.425 Metal complexes: W:H.61, W:H.378 HEA.32: 29 residues within 4Å: Chain W: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, T.316, G.317, V.320, F.348, G.352, L.353, G.355, L.358, S.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain X: I.34, P.69, I.72, L.73 31 PLIP interactions: 26 interactions with chain W, 5 interactions with chain X, Hydrophobic interactions: W:W.126, W:W.236, W:V.243, W:V.243, W:I.247, W:T.309, W:T.316, W:V.320, W:F.348, W:L.353, W:V.373, W:F.377, W:F.377, W:V.380, W:L.381, W:L.381, X:I.34, X:I.34, X:P.69, X:I.72, X:L.73 Hydrogen bonds: W:W.126, W:Y.244, W:D.369 Salt bridges: W:H.368, W:R.438 pi-Stacking: W:H.376, W:H.376 pi-Cation interactions: W:H.240, W:H.291 Metal complexes: W:H.376

1 x MG: MAGNESIUM ION(Non-covalent)

MG.36: 2 residues within 4Å: Chain W: Y.129 Chain X: E.198 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:E.198, X:E.198

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

CUA.38: 6 residues within 4Å: Chain X: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain X Metal complexes: X:H.161, X:C.196, X:C.196, X:E.198, X:C.200, X:C.200, X:H.204

1 x ZN: ZINC ION(Non-covalent)

ZN.41: 5 residues within 4Å: Chain 1: C.61, C.63, C.83, N.85, C.86 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.61, 1:C.63, 1:C.83, 1:C.86

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: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 7: FP
Cytochrome b-c1 complex subunit 8: GQ
Cytochrome b-c1 complex subunit 6, mitochondrial: HR
Cytochrome b-c1 complex subunit 9: IS
Cytochrome b-c1 complex subunit 10: JT
Cytochrome b-c1 complex subunit 9: U
Cox7a2l protein: V
Cytochrome c oxidase subunit 1: W
Cytochrome c oxidase subunit 2: X
Cytochrome c oxidase subunit 3: Y
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: Z
Cytochrome c oxidase subunit 5A, mitochondrial: 0
Cytochrome c oxidase subunit 5B, mitochondrial: 1
Cytochrome c oxidase subunit 6A2, mitochondrial: 2
Cytochrome c oxidase subunit 6B1: 3
Cytochrome c oxidase subunit 6C: 4
Cytochrome c oxidase subunit 7B, mitochondrial: 5
Cytochrome c oxidase subunit 7C, mitochondrial: 6
Cytochrome c oxidase subunit 8B, mitochondrial: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
L

B
B

L
M

C
C

M
N

D
D

N
O

E
E

O
P

F
F

P
Q

G
G

Q
R

H
H

R
S

I
J

S
U

J
K

T
V

U
T

V
I

W
a

X
b

Y
c

Z
d

0
e

1
f

2
g

3
h

4
i

5
k

6
l

7
m

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 Rieske, 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 9

Cytochrome b-c1 complex subunit 10

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

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