SMTL ID : 7o3h.1

Murine CIII2 focus-refined from supercomplex CICIII2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 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, PC1.12 6 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:S.439, A:F.442 Hydrophobic interactions: C:I.229 Salt bridges: C:H.221, C:H.221, D:K.226 3PE.5: 17 residues within 4Å: Chain C: W.30, F.95, L.96, G.99, R.100, L.102, Y.103, Y.104, L.301, M.316, Q.322, Y.325, W.326, L.332 Chain G: R.44, V.48 Ligands: CDL.9 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.30, C:L.96, C:L.102, C:Y.103, C:Y.103, C:L.301, C:W.326, C:L.332 Hydrogen bonds: C:Y.103, C:Y.104, C:Y.104 Salt bridges: G:R.44 3PE.7: 17 residues within 4Å: Chain C: V.43, M.82, L.233, F.236, M.240 Chain D: M.204, K.207, M.208, M.211, M.212, L.215 Chain E: Y.49, A.50, N.53, V.54, Q.57 Chain I: D.36 10 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C, 4 interactions with chain E Hydrophobic interactions: D:M.211, D:L.215, C:V.43, C:L.233, C:F.236, E:Y.49, E:A.50 Salt bridges: D:K.207 Hydrogen bonds: E:N.53, E:Q.57 3PE.11: 15 residues within 4Å: Chain C: P.319, I.320, I.323, I.327, I.334, L.353, A.354, S.357 Chain F: W.19 Chain G: R.42, E.43, L.46, R.47, V.54, I.58 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:I.323, C:I.323, C:I.327, C:I.327, C:I.334, C:L.353, G:I.58 Salt bridges: G:R.47 3PE.13: 8 residues within 4Å: Chain K: S.439, F.442, L.444 Chain M: H.221, T.225, I.229 Ligands: CDL.17, PC1.22 6 PLIP interactions: 4 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: M:T.225, M:I.229 Salt bridges: M:H.221, M:H.221 Hydrogen bonds: K:S.439, K:S.439 3PE.16: 19 residues within 4Å: Chain M: W.30, F.95, L.96, V.98, G.99, R.100, L.102, Y.103, Y.104, F.276, L.301, M.316, Q.322, Y.325, W.326, V.329, L.332 Chain Q: R.44 Ligands: CDL.23 16 PLIP interactions: 15 interactions with chain M, 1 interactions with chain Q Hydrophobic interactions: M:W.30, M:W.30, M:F.95, M:V.98, M:L.102, M:Y.103, M:Y.103, M:F.276, M:L.301, M:W.326, M:W.326, M:V.329 Hydrogen bonds: M:Y.103, M:Y.103, M:Y.104 Salt bridges: Q:R.44 3PE.19: 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, V.54, Q.57 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:M.211, O:V.54 Salt bridges: N:H.200, N:K.207 Hydrogen bonds: O:Q.57 3PE.24: 15 residues within 4Å: Chain M: P.319, I.320, I.323, I.327, I.334, L.353, A.354, S.357 Chain P: F.16, W.19, A.23 Chain Q: R.42, L.46, R.47, V.54 6 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain M Hydrophobic interactions: Q:L.46, Q:V.54, M:I.323, M:I.327, M:I.327 Salt bridges: Q:R.47

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 10 residues within 4Å: Chain A: F.336, W.443, L.444, R.445 Chain C: N.3, R.5, I.19, H.221, T.225 Ligands: 3PE.1 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.444, C:I.19, C:I.19, C:T.225 Hydrogen bonds: A:L.444, A:R.445, C:N.3 Salt bridges: A:R.445, A:R.445, C:R.5, C:H.221 CDL.9: 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.10 10 PLIP interactions: 5 interactions with chain C, 1 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: C:W.30, C:F.33 Hydrogen bonds: C:S.29, C:S.29, C:W.30, G:T.41 Salt bridges: F:H.72, G:R.40, G:R.40, G:R.40 CDL.10: 20 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, I.92, K.227, G.231, I.234, I.238 Chain D: Y.220, K.223, R.224, K.231 Chain G: Y.29, F.30, G.33, I.34, N.36, R.40 Ligands: CDL.9 15 PLIP interactions: 5 interactions with chain C, 6 interactions with chain G, 4 interactions with chain D Hydrophobic interactions: C:F.33, C:L.36, C:I.92, C:I.234, C:I.238, G:Y.29, G:F.30, G:I.34, D:Y.220 Hydrogen bonds: G:Y.29, G:N.36, G:R.40, D:Y.220, D:R.224 Salt bridges: D:K.223 CDL.17: 10 residues within 4Å: Chain K: F.336, W.443, L.444, R.445 Chain M: R.5, F.18, I.19, H.221 Chain T: W.24 Ligands: 3PE.13 10 PLIP interactions: 2 interactions with chain T, 4 interactions with chain M, 4 interactions with chain K Hydrophobic interactions: T:W.24, T:W.24, M:F.18, M:I.19 Salt bridges: M:R.5, M:H.221, K:R.445 Hydrogen bonds: K:F.442, K:L.444, K:R.445 CDL.18: 21 residues within 4Å: Chain M: S.29, N.32, F.33, 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 Q: Y.29, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.23 12 PLIP interactions: 2 interactions with chain Q, 5 interactions with chain N, 5 interactions with chain M Hydrogen bonds: Q:Y.29, Q:R.40, N:Y.220, N:R.224 Hydrophobic interactions: N:L.216, N:Y.220, M:F.33, M:F.33, M:I.92, M:I.234, M:I.238 Salt bridges: N:K.223 CDL.23: 11 residues within 4Å: Chain M: S.28, S.29, W.30, F.33 Chain P: H.72 Chain Q: V.37, R.40, T.41, R.44 Ligands: 3PE.16, CDL.18 9 PLIP interactions: 1 interactions with chain P, 4 interactions with chain Q, 4 interactions with chain M Salt bridges: P:H.72, Q:R.40, Q:R.40, Q:R.40 Hydrophobic interactions: Q:T.41, M:W.30, M:F.33 Hydrogen bonds: M:S.29, M:S.29

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

HEM.3: 22 residues within 4Å: Chain C: Q.44, I.45, G.48, L.51, Y.55, V.66, R.80, H.83, A.84, A.87, V.123, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:Y.55, C:A.127, C:L.133, C:F.179, C:F.183, C:P.186, C:F.187 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.4: 19 residues within 4Å: Chain C: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, 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:L.119, C:L.120, C:L.197, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.14: 20 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.84, A.87, A.127, G.130, Y.131, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 14 PLIP interactions: 14 interactions with chain M, Hydrophobic interactions: M:Q.44, M:Q.44, M:L.51, M:Y.55, M:A.84, M:F.179, M:F.183, M:P.186, M:F.187 Hydrogen bonds: M:N.255 Salt bridges: M:R.80, M:R.80 Metal complexes: M:H.83, M:H.182 HEM.15: 19 residues within 4Å: Chain M: W.31, G.34, L.37, G.38, L.94, H.97, V.98, R.100, S.106, F.109, 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 M, Hydrophobic interactions: M:L.37, M:L.37, M:L.94, M:W.113, M:L.119, 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.6: 20 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, I.158, 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:I.158, 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.20: 22 residues within 4Å: Chain E: H.161 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 16 PLIP interactions: 1 interactions with chain E, 15 interactions with chain N, Salt bridges: E:H.161, N:R.120 Hydrophobic interactions: N:V.36, N:N.105, N:P.111, N:I.116, N:L.130, N:L.131, N:F.153, N:M.160, N:P.163, N:P.163, N:I.164 Hydrogen bonds: N:Y.126, N:G.159 Metal complexes: N:H.41

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

FES.8: 9 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.139, E:C.158 FES.21: 9 residues within 4Å: Chain O: C.139, H.141, L.142, G.143, C.144, C.158, H.161, S.163, P.175 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

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

PC1.12: 16 residues within 4Å: Chain A: D.417, F.442 Chain D: M.222 Chain E: Y.37, T.40, T.43, T.44, V.47 Chain I: F.14, R.15, T.17, F.20, A.21 Chain J: G.31, W.34 Ligands: 3PE.1 8 PLIP interactions: 4 interactions with chain E, 2 interactions with chain I, 1 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: E:T.43, E:V.47, I:A.21, J:W.34 Hydrogen bonds: E:T.40 pi-Cation interactions: E:Y.37, I:F.20 Salt bridges: A:D.417 PC1.22: 12 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, R.15, T.17, F.20 Ligands: 3PE.13 6 PLIP interactions: 2 interactions with chain S, 1 interactions with chain N, 2 interactions with chain O, 1 interactions with chain K Hydrophobic interactions: S:F.20 pi-Cation interactions: S:F.20, O:Y.37 Salt bridges: N:K.226, K:D.417 Hydrogen bonds: O:T.40

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

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

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

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