SMTL ID : 6q9e.1

Complex III2 focused refinement from Ovine respiratory supercomplex I+III2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 17 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, R.80, H.83, A.87, F.90, A.127, G.130, P.134, H.182, F.183, P.186, N.255 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.51, C:A.87, C:F.90, C:A.127, C:P.134, C:F.183, C:P.186 Hydrogen bonds: C:N.255 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83, C:H.83 Metal complexes: C:H.83, C:H.182 HEM.2: 20 residues within 4Å: Chain C: W.31, G.34, L.37, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, T.123, H.196, L.197, L.200, S.205, N.206 Ligands: U10.7 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.98, C:W.113, C:W.113, C:V.117, C:L.119, C:L.120, C:T.123, C:L.197, 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 pi-Stacking: C:H.97, C:H.97, C:H.196 pi-Cation interactions: C:R.100 Metal complexes: C:H.97 HEM.12: 20 residues within 4Å: Chain M: Q.44, G.48, L.49, L.51, A.52, V.66, R.80, H.83, A.84, A.87, F.90, G.130, Y.131, P.134, F.179, H.182, F.183, P.186, F.187, Y.273 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:Q.44, M:L.51, M:L.51, M:A.52, M:A.84, M:F.90, M:F.179, M:F.183, M:F.187 Salt bridges: M:R.80, M:R.80 pi-Stacking: M:H.83, M:H.182 Metal complexes: M:H.83, M:H.182 HEM.13: 18 residues within 4Å: Chain M: W.31, G.34, L.37, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, H.196, L.200, S.205, N.206 Ligands: U10.16 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:V.98, M:W.113, M:V.117, M:L.119, M:L.120, M:L.200 Hydrogen bonds: M:W.31, M:S.106, M:N.206 Salt bridges: M:R.100, M:R.100 Metal complexes: M:H.97, M:H.196

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

3PE.3: 18 residues within 4Å: Chain C: W.30, F.95, M.96, G.99, Y.103, Y.104, F.276, L.301, M.316, Q.322, F.325, W.326, L.332, L.333, Y.358 Chain G: C.44, V.48 Ligands: CDL.4 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.30, C:W.30, C:F.95, C:Y.103, C:F.276, C:L.301, C:F.325, C:W.326, C:W.326, C:L.332, C:L.333, G:V.48 Hydrogen bonds: C:Y.103, C:Y.104 3PE.9: 6 residues within 4Å: Chain C: Y.75 Chain D: M.203, K.206, M.207 Chain E: N.53, Q.57 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 2 interactions with chain C Salt bridges: D:K.206 Hydrogen bonds: E:Q.57, C:Y.75, C:Y.75 3PE.14: 15 residues within 4Å: Chain M: W.30, F.95, M.96, G.99, Y.103, Y.104, L.301, M.316, Q.322, F.325, W.326, L.332, Y.358 Chain Q: V.48 Ligands: CDL.15 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:W.30, M:W.30, M:Y.103, M:Y.104, M:L.301, M:F.325, M:W.326, M:W.326 Hydrogen bonds: M:Y.103, M:Q.322 3PE.19: 10 residues within 4Å: Chain M: M.240 Chain N: H.199, M.203, K.206, M.210 Chain O: A.50, N.53, V.54, Q.57 Chain T: D.36 4 PLIP interactions: 1 interactions with chain T, 2 interactions with chain N, 1 interactions with chain O Hydrogen bonds: T:D.36 Salt bridges: N:H.199, N:K.206 Hydrophobic interactions: O:V.54

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 10 residues within 4Å: Chain C: S.28, S.29, W.30 Chain F: Q.72 Chain G: V.37, R.40, T.41, C.44 Ligands: 3PE.3, CDL.10 8 PLIP interactions: 4 interactions with chain C, 3 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:W.30, G:V.37 Hydrogen bonds: C:S.29, C:S.29, C:W.30, F:Q.72 Salt bridges: G:R.40, G:R.40 CDL.5: 8 residues within 4Å: Chain C: I.13, N.16, L.197, L.198, H.201 Chain M: A.17, L.197, L.198 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.197 Hydrogen bonds: C:H.201 CDL.10: 17 residues within 4Å: Chain C: S.29, N.32, L.36, G.231, L.234 Chain D: Y.219, K.222, R.223, K.230 Chain F: R.71 Chain G: Y.29, F.30, G.33, N.36, V.37, R.40 Ligands: CDL.4 11 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: C:L.36, D:Y.219, G:F.30 Salt bridges: C:K.227, D:K.222, D:R.223, D:K.230, G:R.40 Hydrogen bonds: D:K.230, D:K.230, G:N.36 CDL.15: 8 residues within 4Å: Chain M: S.28, S.29, W.30 Chain P: Q.72 Chain Q: R.40, T.41 Ligands: 3PE.14, CDL.18 8 PLIP interactions: 6 interactions with chain M, 1 interactions with chain P, 1 interactions with chain Q Hydrophobic interactions: M:W.30, Q:T.41 Hydrogen bonds: M:S.28, M:S.28, M:S.28, M:S.29, M:S.29, P:Q.72 CDL.18: 18 residues within 4Å: Chain M: S.29, N.32, L.230, G.231, L.234 Chain N: L.215, P.216, Y.219, K.222, R.223, K.230 Chain P: Q.72 Chain Q: Y.29, G.33, N.36, V.37, R.40 Ligands: CDL.15 18 PLIP interactions: 4 interactions with chain Q, 10 interactions with chain N, 4 interactions with chain M Hydrophobic interactions: Q:Y.29, N:L.215, N:P.216, N:Y.219, N:Y.219, M:L.230, M:L.230, M:L.234 Hydrogen bonds: Q:Y.29, Q:N.36, N:Y.219, N:R.223, N:K.230, N:K.230 Salt bridges: Q:R.40, N:K.222, N:K.222, M:K.227

3 x U10: UBIQUINONE-10(Non-covalent)

U10.6: 11 residues within 4Å: Chain C: A.125, G.142, V.145, I.146, L.149, P.270, F.274, A.277, Y.278, L.281, L.294 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.125, C:I.146, C:L.149, C:F.274, C:A.277, C:L.294 U10.7: 13 residues within 4Å: Chain C: A.17, F.18, L.21, W.31, S.35, G.38, M.194, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.2 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.197, C:L.197, C:F.220 Hydrogen bonds: C:S.35, C:S.205 U10.16: 15 residues within 4Å: Chain M: A.17, F.18, L.21, W.31, G.34, S.35, L.41, A.190, M.194, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.13 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:F.18, M:L.41, M:A.190, M:L.197 pi-Stacking: M:F.220

2 x HEC: HEME C(Covalent)

HEC.8: 18 residues within 4Å: Chain D: V.36, C.37, S.39, C.40, H.41, A.108, L.109, P.111, L.113, I.116, R.120, Y.126, L.130, F.152, I.157, G.158, M.159, P.162 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:V.36, D:P.111, D:L.113, D:I.116, D:L.130, D:I.157 Hydrogen bonds: D:G.158 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.17: 15 residues within 4Å: Chain N: V.36, C.37, C.40, H.41, N.105, A.108, P.110, I.116, R.120, Y.126, L.130, F.152, G.158, M.159, P.162 9 PLIP interactions: 9 interactions with chain N, Hydrophobic interactions: N:P.110, N:I.116, N:L.130, N:M.159 Hydrogen bonds: N:Y.126 Salt bridges: N:R.120 pi-Stacking: N:H.41, N:H.41 Metal complexes: N:H.41

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

FES.11: 7 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, H.161, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.20: 7 residues within 4Å: Chain O: C.139, H.141, L.142, C.144, C.158, H.161, S.163 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Letts, J.A. et al., Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk. Mol.Cell (2019)

Release Date

2019-08-21

Peptides

Ubiquinol-cytochrome c reductase core protein 1: AK
Ubiquinol-cytochrome c reductase core protein 2: BL
Cytochrome b: CM
Cytochrome c1: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 7: FP
Ubiquinol-cytochrome c reductase complex III subunit VII: GQ
Cytochrome b-c1 complex subunit 6: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
Ubiquinol-cytochrome c reductase, complex III subunit X: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a1

K
a3

B
a2

L
a4

C
b1

M
b2

D
c1

N
c2

E
f1

O
f2

F
d1

P
d2

G
q1

Q
q2

H
h1

R
h2

I
x1

S
x2

J
i1

T
i2

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome c reductase core protein 1

Ubiquinol-cytochrome c reductase core protein 2

Cytochrome b

Cytochrome c1

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Ubiquinol-cytochrome c reductase complex III subunit VII

Cytochrome b-c1 complex subunit 6

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Ubiquinol-cytochrome c reductase, complex III subunit X

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