SMTL ID : 8asj.1

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, S.154 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.129, A:H.131, A:C.149, A:H.152 FES.12: 8 residues within 4Å: Chain E: C.129, H.131, G.133, C.134, C.149, H.152, S.154, Y.156 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:H.131, E:C.149, E:H.152

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

PEE.2: 16 residues within 4Å: Chain A: R.12, D.13, Y.16, Y.17, A.20, G.21, A.24, V.25 Chain B: W.245, P.246, I.250 Chain C: L.273 Chain D: F.88, G.91, A.92 Ligands: PEE.10 11 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:Y.16, A:Y.17, D:F.88, D:F.88, D:A.92, B:W.245, B:W.245, B:P.246 Hydrogen bonds: A:Y.17 Salt bridges: A:R.12, D:R.84 PEE.5: 13 residues within 4Å: Chain B: M.1, L.28, D.31, T.32, V.209, A.210, I.213, W.214, H.217 Chain F: P.24, L.28 Ligands: PEE.10, PEE.16 12 PLIP interactions: 1 interactions with chain F, 11 interactions with chain B Hydrophobic interactions: F:L.28, B:T.32, B:V.209, B:I.213, B:I.213, B:W.214, B:W.214, B:W.214 Hydrogen bonds: B:M.1, B:M.1, B:D.31 Salt bridges: B:H.217 PEE.6: 12 residues within 4Å: Chain A: A.29, A.30, P.33 Chain B: L.57, N.88, G.89, F.91, M.92, L.96 Chain C: A.251, T.254, F.258 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:L.57, B:L.96, C:A.251, C:F.258, A:A.30, A:P.33 Hydrogen bonds: B:N.88, B:G.89 PEE.7: 9 residues within 4Å: Chain B: M.44, L.110, F.113, Y.117, Y.118, R.358, F.367, W.368, A.371 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.110, B:F.113, B:Y.117, B:Y.117, B:Y.118, B:F.367, B:W.368, B:A.371 Hydrogen bonds: B:Y.117, B:Y.117, B:Y.118 Salt bridges: B:R.358 PEE.8: 5 residues within 4Å: Chain B: S.175, W.179 Chain E: W.32, I.35, N.39 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:W.179, B:W.179, B:W.179, B:W.179, B:W.179, E:W.32, E:I.35 PEE.9: 7 residues within 4Å: Chain B: I.15, W.18 Chain F: I.130, I.211, A.344, L.345, W.348 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:I.211, F:A.344, F:L.345, F:W.348, F:W.348, B:W.18 PEE.10: 11 residues within 4Å: Chain B: Y.9, R.12, L.28, A.29, Y.30, T.32, I.33, W.245 Ligands: PEE.2, HEM.3, PEE.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.28, B:A.29, B:W.245, B:W.245 Hydrogen bonds: B:Y.30, B:Y.30 Salt bridges: B:R.12, B:R.12 PEE.13: 16 residues within 4Å: Chain E: A.26, A.29, A.30, P.33, L.34 Chain F: L.57, N.88, G.89, M.92, L.96 Chain G: K.244, A.251, T.254, A.255, F.258, L.259 10 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 5 interactions with chain G Hydrophobic interactions: F:L.57, F:M.92, E:A.30, E:P.33, G:A.255, G:F.258, G:L.259 Hydrogen bonds: F:G.89, G:K.244, G:K.244 PEE.16: 7 residues within 4Å: Chain F: M.1, L.28, T.32, I.213, W.214, H.217 Ligands: PEE.5 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:L.28, F:T.32, F:W.214, F:W.214, F:W.214, F:H.217 Hydrogen bonds: F:M.1 PEE.17: 7 residues within 4Å: Chain F: R.12, E.16, A.29, Y.30, I.33, M.34, W.245 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:A.29, F:W.245 Hydrogen bonds: F:R.12, F:W.245 PEE.18: 5 residues within 4Å: Chain A: W.32, N.39 Chain F: S.175, W.179 Ligands: U10.20 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.179 Hydrogen bonds: F:S.175 PEE.19: 7 residues within 4Å: Chain F: L.345, L.349, T.351, A.398, F.401, A.402, L.405 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.345, F:A.398, F:F.401

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

HEM.3: 24 residues within 4Å: Chain B: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, V.209, H.212, F.216, T.219, G.220, N.221, N.222 Ligands: PEE.10 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.51, B:L.51, B:F.104, B:F.104, B:I.112, B:W.129, B:I.135, B:Y.136, B:V.209, B:V.209, B:F.216, B:F.216 Hydrogen bonds: B:G.48, B:T.219, B:T.219, B:N.222 Salt bridges: B:H.111, B:R.114, B:R.125 Metal complexes: B:H.212 HEM.4: 22 residues within 4Å: Chain B: Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, R.94, H.97, A.98, A.101, T.142, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, Y.297 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:Q.58, B:A.66, B:Y.69, B:A.98, B:A.101, B:T.142, B:L.149, B:L.149, B:F.195, B:Y.199, B:Y.199, B:I.205 Salt bridges: B:R.94, B:R.94 pi-Stacking: B:H.198 Metal complexes: B:H.97, B:H.198 HEM.14: 22 residues within 4Å: Chain F: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, W.129, G.132, M.133, I.135, Y.136, V.209, H.212, F.216, T.219, G.220, N.221, N.222 21 PLIP interactions: 21 interactions with chain F, Hydrophobic interactions: F:L.51, F:L.51, F:F.104, F:I.112, F:W.129, F:W.129, F:I.135, F:Y.136, F:V.209, F:V.209, F:F.216, F:F.216, F:F.216 Hydrogen bonds: F:G.48, F:T.219, F:T.219, F:N.222 Salt bridges: F:H.111, F:R.114, F:R.125 Metal complexes: F:H.212 HEM.15: 20 residues within 4Å: Chain F: Q.58, G.62, I.63, L.65, A.66, Y.69, R.94, H.97, A.98, A.101, T.142, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, I.205, Y.297 16 PLIP interactions: 16 interactions with chain F, Hydrophobic interactions: F:Q.58, F:I.63, F:A.66, F:Y.69, F:A.101, F:T.142, F:L.149, F:L.149, F:Y.199, F:Y.199, F:P.202, F:I.205 Salt bridges: F:R.94, F:R.94 Metal complexes: F:H.97, F:H.198

2 x HEC: HEME C(Covalent)(Non-covalent)

HEC.11: 18 residues within 4Å: Chain C: V.57, C.58, C.61, H.62, L.116, N.118, P.120, L.122, M.125, R.129, Y.152, L.157, F.182, I.205, A.206, M.207, V.233, L.237 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:V.57, C:L.116, C:L.122, C:L.157, C:L.157, C:A.206, C:V.233, C:L.237 Hydrogen bonds: C:Y.152, C:A.206 Salt bridges: C:R.129 Metal complexes: C:H.62 HEC.21: 19 residues within 4Å: Chain G: V.57, C.58, C.61, H.62, L.116, N.118, A.119, P.120, L.122, M.125, R.129, Y.152, L.157, F.182, I.205, A.206, M.207, P.208, P.210 9 PLIP interactions: 9 interactions with chain G, Hydrophobic interactions: G:V.57, G:N.118, G:A.119, G:L.122, G:L.157, G:I.205, G:A.206 Salt bridges: G:R.129 Metal complexes: G:H.62

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

U10.20: 23 residues within 4Å: Chain A: L.34, I.35, M.38, H.152 Chain B: I.63 Chain F: M.140, A.141, F.144, G.158, V.161, I.162, F.166, W.179, L.180, L.197, I.292, P.294, E.295, F.298, F.301, Y.302, L.305 Ligands: PEE.18 17 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: F:M.140, F:F.144, F:I.162, F:I.162, F:F.166, F:F.166, F:W.179, F:W.179, F:L.180, F:L.197, F:P.294, F:P.294, F:F.298, F:F.298, F:F.301, A:I.35, B:I.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swainsbury, D.J.K. et al., Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc 1 complex in styrene maleic acid nanodiscs. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-03-15

Peptides

Ubiquinol-cytochrome c reductase iron-sulfur subunit: AE
Cytochrome b: BF
Cytochrome c1: CG
Cytochrome b-c1 subunit IV: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cytochrome b

Cytochrome c1

Cytochrome b-c1 subunit IV

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