SMTL ID : 9c7h.1

Cryo-EM structure of respiratory supercomplex III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-4-2-2-2-2-2-2-2-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain C: C.242, H.244, L.245, C.247, C.261, C.263, H.264, G.265, S.266 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.242, C:H.244, C:C.261, C:H.264 FES.2: 10 residues within 4Å: Chain E: C.242, H.244, L.245, C.247, C.261, C.263, H.264, G.265, S.266, P.278 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.242, E:H.244, E:C.261, E:H.264

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

HEM.3: 22 residues within 4Å: Chain H: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, R.80, H.83, A.87, F.90, T.126, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 16 PLIP interactions: 16 interactions with chain H, Hydrophobic interactions: H:L.41, H:Q.44, H:L.49, H:L.51, H:L.51, H:Y.55, H:F.90, H:T.126, H:L.133, H:L.133, H:F.179, H:F.183 Salt bridges: H:R.80, H:R.80 Metal complexes: H:H.83, H:H.182 HEM.4: 25 residues within 4Å: Chain H: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, L.119, L.120, V.123, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 26 PLIP interactions: 26 interactions with chain H, Hydrophobic interactions: H:L.37, H:L.37, H:F.90, H:V.98, H:T.112, H:W.113, H:W.113, H:W.113, H:L.119, H:L.119, H:L.120, H:V.123, H:I.189, H:A.193, H:L.197, H:L.200, H:L.301 Hydrogen bonds: H:W.31, H:G.34, H:S.106, H:N.206 Salt bridges: H:H.97, H:R.100, H:R.100 pi-Cation interactions: H:R.100 Metal complexes: H:H.196 HEM.6: 22 residues within 4Å: Chain M: L.41, Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:L.41, M:Q.44, M:L.51, M:L.51, M:Y.55, M:F.90, M:T.126, M:L.133, M:L.133, M:F.179, M:F.183, M:F.183 Salt bridges: M:R.80, M:R.80 Metal complexes: M:H.83 HEM.7: 23 residues within 4Å: Chain M: W.31, G.34, S.35, L.37, F.90, L.94, H.97, V.98, R.100, S.106, F.109, T.112, W.113, G.116, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206 21 PLIP interactions: 21 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:F.90, M:T.112, M:W.113, M:W.113, M:L.119, M:L.120, M:I.189, M:A.193, M:L.197, M:L.200 Hydrogen bonds: M:W.31, M:G.34, M:S.106, M:S.205, M:N.206 Salt bridges: M:H.97, M:R.100, M:R.100 pi-Cation interactions: M:R.100

2 x HEC: HEME C(Covalent)

HEC.5: 19 residues within 4Å: Chain I: V.121, C.122, C.125, H.126, N.190, L.194, P.195, P.196, I.201, R.205, Y.211, L.215, L.216, F.238, I.243, A.244, M.245, P.248, I.249 19 PLIP interactions: 19 interactions with chain I, Hydrophobic interactions: I:V.121, I:N.190, I:P.195, I:P.196, I:I.201, I:L.215, I:L.216, I:L.216, I:I.243, I:A.244, I:M.245, I:P.248, I:P.248, I:I.249 Hydrogen bonds: I:Y.211, I:Y.211, I:A.244 Salt bridges: I:R.205 Metal complexes: I:H.126 HEC.8: 23 residues within 4Å: Chain N: V.121, C.122, C.125, H.126, N.190, A.193, P.195, P.196, L.198, I.201, R.205, Y.211, V.212, L.215, L.216, F.238, I.243, A.244, M.245, P.248, I.249, V.271, L.275 20 PLIP interactions: 20 interactions with chain N, Hydrophobic interactions: N:V.121, N:N.190, N:A.193, N:P.196, N:L.198, N:I.201, N:V.212, N:L.215, N:L.216, N:I.243, N:A.244, N:M.245, N:P.248, N:I.249, N:V.271, N:L.275 Hydrogen bonds: N:A.244 Salt bridges: N:R.205 pi-Stacking: N:H.126 Metal complexes: N:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cryo-EM structure of respiratory supercomplex III. To Be Published

Release Date

2025-07-02

Peptides

Cytochrome b-c1 complex subunit 6, mitochondrial: AT
Ubiquinol-cytochrome c reductase complex 7.2 kDa protein: BU
Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1: CEQR
Cytochrome b-c1 complex subunit 10: DV
Cytochrome b-c1 complex subunit 1, mitochondrial: FK
Cytochrome b-c1 complex subunit 2, mitochondrial: GL
Cytochrome b: HM
Cytochrome c1: IN
Cytochrome b-c1 complex subunit 7: JO
Cytochrome b-c1 complex subunit 8: PS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

T
Ab

B
1

U
Ac

C
2

E
4

Q
Af

R
Ae

D
3

V
Ad

F
5

K
u

G
6

L
v

H
7

M
w

I
8

N
x

J
9

O
y

P
z

S
Aa

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 6, mitochondrial

Ubiquinol-cytochrome c reductase complex 7.2 kDa protein

Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1

Cytochrome b-c1 complex subunit 10

Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

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