SMTL ID : 7jrg.1

Plant Mitochondrial complex III2 from Vigna radiata

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.137, H.141, E.217 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.137, A:H.141, A:E.217, A:E.217 ZN.19: 3 residues within 4Å: Chain K: H.137, H.141, E.217 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.137, K:H.141, K:E.217, K:E.217

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

PC1.2: 13 residues within 4Å: Chain A: Y.497, D.498, Y.523, N.525 Chain E: Y.112, R.119 Chain I: M.21, N.24, Y.27, V.28 Chain J: Y.31 Ligands: CDL.3, CDL.4 10 PLIP interactions: 2 interactions with chain I, 3 interactions with chain E, 1 interactions with chain J, 4 interactions with chain A Hydrogen bonds: I:N.24, A:Y.523, A:N.525 pi-Cation interactions: I:Y.27, E:Y.112, A:Y.523 Salt bridges: E:R.119, E:R.119, A:D.498 Hydrophobic interactions: J:Y.31 PC1.22: 13 residues within 4Å: Chain K: Y.497, D.498, Y.523, N.525 Chain O: Y.112, R.119, I.126 Chain S: Y.27, V.28, V.31, I.32 Ligands: CDL.21, CDL.24 13 PLIP interactions: 5 interactions with chain O, 4 interactions with chain S, 4 interactions with chain K Hydrophobic interactions: O:I.126, O:I.126, S:V.28, S:V.31, S:I.32 Salt bridges: O:R.119, O:R.119, K:D.498 pi-Cation interactions: O:Y.112, S:Y.27, K:Y.523 Hydrogen bonds: K:Y.523, K:N.525 PC1.34: 9 residues within 4Å: Chain N: L.279, Y.286 Chain O: F.110, V.114, V.121 Chain Q: K.21, V.22, M.23, W.27 6 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain O, 1 interactions with chain N Hydrogen bonds: Q:V.22, Q:M.23 Hydrophobic interactions: O:V.114, O:V.114, O:V.121, N:L.279

9 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 18 residues within 4Å: Chain A: Y.417, Q.421, R.520, R.521, W.524, N.525, R.526 Chain C: S.9, L.10, L.11, I.24, I.44, F.227, Y.228, W.239 Chain J: W.21 Ligands: PC1.2, CDL.4 16 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J, 9 interactions with chain A Hydrophobic interactions: C:I.24, C:I.44, C:Y.228, C:Y.228, C:W.239, J:W.21, A:N.525 Hydrogen bonds: C:S.9, A:Y.523, A:N.525, A:R.526 Salt bridges: A:R.520, A:R.521, A:R.521, A:R.526, A:R.526 CDL.4: 17 residues within 4Å: Chain A: R.520, N.525 Chain C: V.47, I.48, Y.228, Y.232, L.236, W.239, A.243 Chain D: Y.287 Chain E: R.119, Y.122, A.123, I.126, L.129 Ligands: PC1.2, CDL.3 17 PLIP interactions: 6 interactions with chain C, 6 interactions with chain E, 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: C:V.47, C:I.48, C:I.48, C:Y.232, C:W.239, C:A.243, E:Y.122, E:A.123, E:I.126, E:L.129 Hydrogen bonds: E:R.119, D:Y.287, D:Y.287, D:Y.287, A:N.525 Salt bridges: E:R.119, A:R.520 CDL.13: 15 residues within 4Å: Chain C: S.33, Y.34, W.35, F.38, Y.109, A.241, F.242 Chain F: H.76 Chain G: K.37, E.40, N.41, W.42, A.45 Ligands: 3PE.12, CDL.15 11 PLIP interactions: 1 interactions with chain F, 5 interactions with chain C, 5 interactions with chain G Salt bridges: F:H.76, G:K.37 Hydrophobic interactions: C:W.35, C:W.35, C:A.241, G:N.41, G:W.42, G:A.45 Hydrogen bonds: C:Y.34, C:Y.109, G:N.41 CDL.15: 13 residues within 4Å: Chain C: Y.34, I.248 Chain D: S.278, L.281, L.282, A.285, R.288, R.289 Chain G: L.26, L.30, K.37 Ligands: 3PE.10, CDL.13 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: D:L.281, C:I.248 Hydrogen bonds: D:R.289 Salt bridges: D:R.288, G:K.37, G:K.37 CDL.21: 19 residues within 4Å: Chain K: Y.417, Q.421, R.520, R.521, W.524, N.525, R.526 Chain M: S.9, L.11, L.23, I.24, S.40, L.204, Y.228, W.239 Chain T: W.21 Ligands: 3PE.20, PC1.22, CDL.24 13 PLIP interactions: 7 interactions with chain M, 5 interactions with chain K, 1 interactions with chain T Hydrophobic interactions: M:L.11, M:L.23, M:L.204, M:Y.228, M:W.239, T:W.21 Hydrogen bonds: M:S.9, M:S.9, K:N.525, K:R.526 Salt bridges: K:R.520, K:R.521, K:R.526 CDL.24: 20 residues within 4Å: Chain K: R.520, N.525 Chain M: I.44, I.48, Y.228, Y.232, L.236, W.239, A.243, F.246, F.251 Chain N: Y.287 Chain O: R.119, Y.122, L.125, I.126, L.128, V.130 Ligands: CDL.21, PC1.22 22 PLIP interactions: 12 interactions with chain M, 6 interactions with chain O, 2 interactions with chain K, 2 interactions with chain N Hydrophobic interactions: M:I.44, M:I.48, M:I.48, M:Y.232, M:L.236, M:W.239, M:W.239, M:A.243, M:F.246, M:F.251, M:F.251, O:Y.122, O:L.125, O:I.126, O:L.128, O:V.130 Hydrogen bonds: M:Y.232, K:N.525, N:Y.287, N:Y.287 Salt bridges: O:R.119, K:R.520 CDL.28: 16 residues within 4Å: Chain M: Y.100, F.104, F.245, W.249, V.256, L.257, H.259, W.279, L.282, P.283, L.308, C.339, G.343, W.344, C.347, Q.348 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:Y.100, M:F.104, M:F.245, M:W.249, M:V.256, M:W.279, M:L.282, M:L.308 CDL.33: 14 residues within 4Å: Chain M: Y.34, F.38, F.242 Chain N: A.285, R.288, R.289 Chain Q: M.23, L.26, W.27, L.30, K.33, I.34, K.37 Ligands: CDL.35 9 PLIP interactions: 1 interactions with chain P, 3 interactions with chain M, 2 interactions with chain N, 3 interactions with chain Q Salt bridges: P:H.76, N:R.288, N:R.289, Q:K.33, Q:K.37, Q:K.37 Hydrophobic interactions: M:Y.34, M:F.38, M:F.38 CDL.35: 12 residues within 4Å: Chain M: S.33, Y.34, W.35, F.38 Chain P: H.76 Chain Q: K.37, V.38, N.41, A.45, T.46 Ligands: 3PE.30, CDL.33 9 PLIP interactions: 1 interactions with chain P, 5 interactions with chain Q, 3 interactions with chain M Salt bridges: P:H.76, Q:K.37 Hydrophobic interactions: Q:V.38, Q:N.41, Q:A.45, Q:T.46, M:W.35, M:F.38 Hydrogen bonds: M:Y.34

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

HEM.5: 20 residues within 4Å: Chain C: L.46, Q.49, I.50, G.53, V.54, L.56, Y.60, R.85, H.88, A.92, A.134, G.137, Y.138, L.140, P.141, H.189, Y.190, P.193, F.194, Y.280 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.46, C:Q.49, C:L.56, C:Y.60, C:L.140, C:L.140, C:Y.190, C:P.193, C:F.194 Salt bridges: C:R.85, C:R.85 pi-Stacking: C:H.88, C:H.189 Metal complexes: C:H.88, C:H.189 HEM.6: 21 residues within 4Å: Chain C: W.36, G.39, A.42, G.43, F.95, V.99, H.102, I.103, R.105, S.111, V.119, W.120, G.123, V.124, I.126, S.200, H.203, L.204, L.207, S.212, N.213 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:A.42, C:F.95, C:V.99, C:I.103, C:V.119, C:W.120, C:V.124, C:I.126, C:L.207 Hydrogen bonds: C:W.36, C:G.39, C:S.111, C:S.212, C:S.212, C:N.213 Salt bridges: C:H.102, C:R.105, C:R.105, C:R.116 pi-Cation interactions: C:R.105 Metal complexes: C:H.102, C:H.203 HEM.25: 22 residues within 4Å: Chain M: Q.49, I.50, G.53, V.54, L.56, A.57, Y.60, V.71, R.85, H.88, A.89, A.92, F.95, A.134, G.137, Y.138, L.140, P.141, H.189, Y.190, P.193, Y.280 12 PLIP interactions: 12 interactions with chain M, Hydrophobic interactions: M:Q.49, M:L.56, M:Y.60, M:A.89, M:F.95, M:L.140, M:Y.190, M:P.193 Salt bridges: M:R.85, M:R.85 Metal complexes: M:H.88, M:H.189 HEM.26: 19 residues within 4Å: Chain M: W.36, G.39, G.43, F.95, V.99, H.102, I.103, R.105, S.111, W.120, G.123, V.124, I.126, S.200, H.203, L.204, L.207, S.212, N.213 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:F.95, M:V.99, M:W.120, M:W.120, M:V.124, M:I.126, M:L.207 Hydrogen bonds: M:W.36, M:W.36, M:G.39, M:S.111, M:N.213 Salt bridges: M:H.102, M:R.105, M:R.105 pi-Cation interactions: M:R.105 Metal complexes: M:H.102, M:H.203

17 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.7: 10 residues within 4Å: Chain C: P.14, I.15, S.17, T.18 Chain M: F.118, G.198, L.202, A.205, Q.209 Chain P: P.122 Ligand excluded by PLIP 3PE.8: 15 residues within 4Å: Chain C: F.324, R.325, P.326, I.327, Y.328, I.374, L.375, V.378, G.379, I.382 Chain F: L.16, H.20, L.24, Y.35 Ligands: 3PE.16 Ligand excluded by PLIP 3PE.9: 13 residues within 4Å: Chain C: Y.100, F.104, W.279, L.282, P.283, G.343, W.344, C.347, Q.348, F.365 Chain G: L.52, Y.56 Ligands: 3PE.11 Ligand excluded by PLIP 3PE.10: 8 residues within 4Å: Chain C: I.248, W.249, A.253 Chain D: I.82, F.271, I.274 Ligands: 3PE.11, CDL.15 Ligand excluded by PLIP 3PE.11: 9 residues within 4Å: Chain C: V.256, L.257, G.258, H.259, P.260, W.279 Chain D: H.186 Ligands: 3PE.9, 3PE.10 Ligand excluded by PLIP 3PE.12: 15 residues within 4Å: Chain C: W.35, L.101, F.104, Y.108, Y.109, S.323, F.332, W.333, L.336 Chain F: Y.31, Y.78 Chain G: N.41, S.44, L.48 Ligands: CDL.13 Ligand excluded by PLIP 3PE.16: 11 residues within 4Å: Chain C: P.326, I.327, I.331 Chain F: L.16, Q.19, H.20, S.23, K.26, R.27 Chain G: I.43 Ligands: 3PE.8 Ligand excluded by PLIP 3PE.17: 9 residues within 4Å: Chain C: F.118, C.121, I.306, L.309, F.313 Chain F: Q.118, R.119, P.122 Chain M: R.7 Ligand excluded by PLIP 3PE.18: 9 residues within 4Å: Chain D: L.279, Y.286 Chain E: F.110, V.114, G.117 Chain G: K.21, V.22, M.23, T.24 Ligand excluded by PLIP 3PE.20: 6 residues within 4Å: Chain F: I.121 Chain K: R.526 Chain M: L.10 Chain T: W.21, A.25 Ligands: CDL.21 Ligand excluded by PLIP 3PE.23: 7 residues within 4Å: Chain C: F.118, L.202, A.205, Q.209 Chain M: P.14, I.15, T.18 Ligand excluded by PLIP 3PE.27: 6 residues within 4Å: Chain E: L.131, V.134 Chain J: L.32 Chain M: T.166, I.167, W.170 Ligand excluded by PLIP 3PE.29: 11 residues within 4Å: Chain M: F.245, I.248, W.249, Y.252, A.253 Chain N: K.80, G.81, I.82, F.271, I.274, S.278 Ligand excluded by PLIP 3PE.30: 13 residues within 4Å: Chain M: W.35, Y.108, Y.109, S.323, Q.329, W.333, L.336 Chain P: Y.31, Y.78 Chain Q: N.41, L.48, L.49 Ligands: CDL.35 Ligand excluded by PLIP 3PE.31: 15 residues within 4Å: Chain M: P.326, I.327, G.330, I.331, L.334, V.364, L.367, F.368, I.371 Chain P: Q.19, H.20, S.23, K.26, R.27 Chain Q: I.43 Ligand excluded by PLIP 3PE.36: 7 residues within 4Å: Chain C: T.166, W.170 Chain O: L.131, V.134, L.135 Chain T: V.33 Ligands: 3PE.37 Ligand excluded by PLIP 3PE.37: 9 residues within 4Å: Chain C: V.163, T.166 Chain T: V.33, Q.34, V.35, S.36, I.37, L.38 Ligands: 3PE.36 Ligand excluded by PLIP

2 x HEC: HEME C(Covalent)

HEC.14: 19 residues within 4Å: Chain D: V.101, C.102, C.105, H.106, N.170, A.173, Y.174, P.175, P.176, I.181, R.185, Y.191, L.195, L.196, F.218, A.224, M.225, M.228, V.251 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:V.101, D:N.170, D:A.173, D:P.175, D:P.176, D:I.181, D:L.195, D:L.196, D:L.196, D:F.218, D:A.224, D:M.225, D:V.251 Hydrogen bonds: D:Y.191, D:Y.191, D:A.224 Salt bridges: D:R.185 pi-Stacking: D:H.106, D:H.106 Metal complexes: D:H.106 HEC.32: 18 residues within 4Å: Chain N: V.101, C.102, C.105, H.106, N.170, A.173, Y.174, P.175, P.176, I.181, R.185, Y.191, L.195, L.196, F.218, A.224, M.225, M.228 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.101, N:N.170, N:P.175, N:P.176, N:I.181, N:L.195, N:L.196, N:L.196, N:F.218, N:A.224 Hydrogen bonds: N:Y.191, N:Y.191 Salt bridges: N:R.185 pi-Stacking: N:H.106, N:H.106 Metal complexes: N:H.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maldonado, M. et al., Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants. Elife (2021)

Release Date

2021-01-20

Peptides

Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1: AK
Alpha-MPP: BL
COB: CM
cytochrome c1-2, 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: HR
cytochrome b-c1 complex subunit 9: IS
QCR10: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
M

B
B

L
N

C
C

M
O

D
D

N
P

E
E

O
Q

F
F

P
R

G
G

Q
S

H
H

R
T

I
J

S
V

J
K

T
W

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1

Alpha-MPP

COB

cytochrome c1-2, 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

cytochrome b-c1 complex subunit 9

QCR10

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