SMTL ID : 8iog.1

Cryo-EM structure of porcine bc1 complex in isolated state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 13 residues within 4Å: Chain A: W.31, G.34, L.37, H.97, V.98, R.100, S.106, W.113, G.116, H.196, L.197, S.205, N.206 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:L.37, A:L.197 Hydrogen bonds: A:S.106, A:N.206 Salt bridges: A:R.100, A:R.100 Metal complexes: A:H.97, A:H.196 HEM.2: 15 residues within 4Å: Chain A: Q.44, G.48, L.51, R.80, H.83, A.84, A.87, F.90, G.130, L.133, F.179, H.182, F.183, P.186, Y.273 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:A.87, A:F.90, A:L.133, A:L.133, A:F.179, A:F.183, A:P.186 Salt bridges: A:R.80, A:R.80 Metal complexes: A:H.83 HEM.8: 15 residues within 4Å: Chain L: G.48, L.49, L.51, A.52, V.66, R.80, H.83, G.130, Y.131, L.133, F.179, H.182, F.183, P.186, F.187 10 PLIP interactions: 10 interactions with chain L, Hydrophobic interactions: L:L.49, L:L.51, L:A.52, L:L.133, L:F.179, L:F.183, L:F.183, L:P.186 Salt bridges: L:R.80 Metal complexes: L:H.182 HEM.9: 12 residues within 4Å: Chain L: W.31, H.97, V.98, R.100, S.106, W.113, G.116, L.119, L.120, H.196, L.200, S.205 12 PLIP interactions: 12 interactions with chain L, Hydrophobic interactions: L:V.98, L:W.113, L:W.113, L:L.119, L:L.120, L:L.200 Hydrogen bonds: L:S.106, L:S.106 Salt bridges: L:H.97, L:R.100, L:R.100 Metal complexes: L:H.196

3 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.3: 10 residues within 4Å: Chain A: W.30, F.95, I.96, V.98, Y.103, Y.104, M.316, Q.322, W.326, V.329 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.96, A:V.98 Hydrogen bonds: A:Y.104, A:Y.104, A:Q.322 PEE.7: 6 residues within 4Å: Chain A: H.221 Chain C: V.47 Chain D: S.473, F.476, L.478 Ligands: CDL.6 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:S.473, D:L.478 Hydrophobic interactions: C:V.47 Salt bridges: A:H.221 PEE.10: 15 residues within 4Å: Chain L: W.30, F.95, Y.103, Y.104, M.316, F.325, W.326, L.328, V.329, L.332, I.333 Chain S: C.45, R.48, V.49 Ligands: CDL.11 11 PLIP interactions: 1 interactions with chain S, 10 interactions with chain L Hydrogen bonds: S:R.48 Hydrophobic interactions: L:F.95, L:Y.103, L:Y.103, L:F.325, L:F.325, L:W.326, L:L.328, L:V.329, L:V.329, L:I.333

2 x HEC: HEME C(Non-covalent)

HEC.4: 16 residues within 4Å: Chain B: V.121, C.122, C.125, H.126, N.190, A.193, L.194, P.195, P.196, L.198, L.215, I.243, M.245, P.248, I.249, V.271 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.121, B:L.198, B:L.198, B:L.215, B:P.248, B:I.249, B:V.271 Hydrogen bonds: B:L.194 Metal complexes: B:H.126 HEC.12: 15 residues within 4Å: Chain M: C.122, C.125, H.126, N.190, A.193, L.194, P.196, R.205, L.215, F.238, I.243, A.244, M.245, P.248, I.249 11 PLIP interactions: 11 interactions with chain M, Hydrophobic interactions: M:N.190, M:P.196, M:L.215, M:I.243, M:A.244, M:P.248, M:P.248, M:I.249 Hydrogen bonds: M:A.244 Salt bridges: M:R.205 pi-Stacking: M:H.126

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

FES.5: 6 residues within 4Å: Chain C: C.139, L.142, G.143, C.144, C.160, H.161 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.139, C:C.144, C:C.144 FES.13: 6 residues within 4Å: Chain N: C.139, H.141, L.142, C.144, C.160, H.161 1 PLIP interactions: 1 interactions with chain N, Metal complexes: N:C.144

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 10 residues within 4Å: Chain A: R.5, M.11, I.14, F.18, I.19, H.221 Chain D: W.477, L.478, R.479 Ligands: PEE.7 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.14 Salt bridges: A:R.5, A:H.221 Hydrogen bonds: D:L.478, D:R.479, D:R.479 CDL.11: 10 residues within 4Å: Chain L: S.29, W.30, F.33, M.89 Chain R: Q.73 Chain S: R.41, T.42, C.45, I.46 Ligands: PEE.10 6 PLIP interactions: 4 interactions with chain S, 1 interactions with chain R, 1 interactions with chain L Hydrophobic interactions: S:T.42, S:I.46 Salt bridges: S:R.41, S:R.41 Hydrogen bonds: R:Q.73, L:S.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.X. et al., Cryo-EM structure of porcine bc1 complex in isolated state. To Be Published

Release Date

2024-04-17

Peptides

Cytochrome b: AL
Cytochrome c1, heme protein, mitochondrial: BM
Cytochrome b-c1 complex subunit Rieske, mitochondrial: CN
Cytochrome b-c1 complex subunit 1, mitochondrial: DO
Cytochrome b-c1 complex subunit 2, mitochondrial: EP
Cytochrome b-c1 complex subunit 6: FQ
Cytochrome b-c1 complex subunit 7: GR
Cytochrome b-c1 complex subunit 8: HS
Complex III subunit 9: IT
Cytochrome b-c1 complex subunit 10: JU
Cytochrome b-c1 complex subunit Rieske, mitochondrial: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
a

B
B

M
b

C
C

N
c

D
D

O
d

E
E

P
e

F
F

Q
f

G
G

R
g

H
H

S
h

I
I

T
i

J
J

U
j

K
K

V
k

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b-c1 complex subunit 6

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Complex III subunit 9

Cytochrome b-c1 complex subunit 10

Cytochrome b-c1 complex subunit Rieske, mitochondrial

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