SMTL ID : 9f5z.1

Structure of the Chlamydomonas reinhardtii respiratory complex III from respiratory supercomplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x UQ5: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE(Non-covalent)

UQ5.1: 11 residues within 4Å: Chain A: T.22, L.26, W.30, S.34, G.37, H.202, S.206, F.221, F.225, D.229 Ligands: HEC.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.221, A:F.221 Hydrogen bonds: A:S.34 UQ5.2: 17 residues within 4Å: Chain A: I.125, I.126, F.129, I.130, Y.132, G.143, I.147, L.165, F.179, F.182, L.186, I.269, V.270, P.271, F.275, V.278, Y.279 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.125, A:I.126, A:F.129, A:F.129, A:I.147, A:I.147, A:L.165, A:L.165, A:F.179, A:F.179, A:F.182, A:F.182, A:F.182, A:L.186, A:P.271, A:P.271, A:F.275, A:V.278, A:Y.279 UQ5.7: 19 residues within 4Å: Chain A: I.189 Chain B: H.16, L.17, T.22, W.30, S.34, G.37, L.40, A.41, M.44, S.194, V.195, I.198, H.202, F.221, D.229 Ligands: HEC.10, CDL.14, CDL.15 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.189, B:L.17, B:L.40, B:L.40, B:V.195, B:I.198, B:F.221 UQ5.8: 16 residues within 4Å: Chain B: I.125, I.126, F.129, Y.132, M.139, G.143, I.147, L.165, F.182, I.269, V.270, P.271, E.272, F.275, V.278, Y.279 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.125, B:I.126, B:I.126, B:F.129, B:I.147, B:I.147, B:L.165, B:F.182, B:F.182, B:P.271, B:P.271, B:F.275, B:Y.279

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

HEC.3: 19 residues within 4Å: Chain A: Q.43, M.44, G.47, I.48, L.50, R.79, H.82, A.86, F.89, M.124, G.131, Y.132, L.134, P.135, Y.180, H.183, Y.184, P.187, Y.274 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:Q.43, A:A.86, A:F.89, A:L.134, A:L.134, A:Y.180, A:Y.184, A:P.187 Salt bridges: A:R.79, A:R.79 Metal complexes: A:H.82, A:H.183 HEC.4: 22 residues within 4Å: Chain A: W.30, G.32, G.33, S.34, A.36, G.37, F.89, V.93, H.96, V.97, R.99, S.105, V.113, W.114, G.117, V.118, I.120, H.197, L.201, S.206, T.207 Ligands: UQ5.1 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:A.36, A:F.89, A:V.93, A:V.97, A:V.113, A:W.114, A:W.114, A:V.118, A:I.120, A:L.201, A:L.201 Hydrogen bonds: A:G.32, A:G.33, A:S.206, A:T.207 Salt bridges: A:H.96, A:R.99, A:R.99 pi-Stacking: A:H.96 Metal complexes: A:H.197 HEC.9: 21 residues within 4Å: Chain B: L.40, Q.43, M.44, G.47, I.48, L.50, R.79, H.82, A.86, F.90, T.127, A.128, G.131, Y.132, L.134, P.135, Y.180, H.183, Y.184, P.187, Y.274 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:L.40, B:Q.43, B:F.90, B:T.127, B:A.128, B:L.134, B:L.134, B:Y.180, B:Y.184, B:P.187, B:P.187 Water bridges: B:R.79, B:R.79 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.82, B:H.183 HEC.10: 23 residues within 4Å: Chain B: W.30, G.32, G.33, S.34, A.36, G.37, F.89, V.93, H.96, V.97, R.99, S.105, V.113, G.117, V.118, I.120, S.194, H.197, I.198, L.201, S.206, T.207 Ligands: UQ5.7 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.36, B:F.89, B:V.93, B:V.97, B:V.113, B:V.118, B:I.120, B:I.198, B:L.201 Hydrogen bonds: B:G.33, B:S.105, B:T.207 Water bridges: B:G.32 Salt bridges: B:H.96, B:R.99, B:R.99 Metal complexes: B:H.96, B:H.197 HEC.18: 19 residues within 4Å: Chain E: V.109, C.110, C.113, H.114, N.178, P.183, P.184, I.189, R.193, Y.199, L.203, L.204, F.226, I.231, A.232, M.233, P.234, M.236, L.237 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:V.109, E:P.183, E:I.189, E:L.203, E:L.204, E:I.231, E:P.234, E:M.236, E:L.237 Hydrogen bonds: E:Y.199, E:Y.199, E:A.232 Salt bridges: E:R.193 Metal complexes: E:H.114 HEC.20: 20 residues within 4Å: Chain F: V.109, C.110, C.113, H.114, N.178, Y.182, P.183, P.184, L.186, I.189, R.193, Y.199, L.203, L.204, F.226, I.231, A.232, M.233, P.234, M.236 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:V.109, F:V.109, F:P.184, F:L.186, F:I.189, F:L.203, F:L.204, F:I.231, F:A.232, F:P.234 Hydrogen bonds: F:Y.199, F:A.232 Salt bridges: F:R.193 Metal complexes: F:H.114

8 x CDL: CARDIOLIPIN(Non-covalent)(Covalent)

CDL.5: 17 residues within 4Å: Chain A: N.27, Y.28, S.29, L.35, L.95, R.99, Y.102, Y.103, G.232, F.235, Y.323, W.324 Chain L: T.34, F.38, K.42 Chain R: H.76 Ligands: CDL.27 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain L Hydrophobic interactions: A:Y.28, A:L.35, A:F.235, A:F.235, L:F.38, L:F.38 Hydrogen bonds: A:N.27, A:N.27, A:Y.28, A:S.29, A:Y.103 Salt bridges: L:K.42, L:K.42 CDL.11: 17 residues within 4Å: Chain B: N.27, Y.28, S.29, G.32, L.95, L.98, R.99, Y.102, Y.103, F.235, K.314, Y.323, W.324 Chain K: F.38, K.42 Chain T: H.76 Ligands: CDL.24 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain K Hydrophobic interactions: B:N.27, B:Y.28, B:Y.28, B:F.235, B:F.235, K:F.38 Hydrogen bonds: B:N.27, B:S.29, B:Y.103, B:Y.323 Water bridges: B:G.32 Salt bridges: B:K.314, K:K.42, K:K.42 CDL.14: 16 residues within 4Å: Chain A: Q.8, V.12, H.16, G.192, F.196, A.199 Chain B: Q.8, V.12, H.16, G.192, V.195, F.196, A.199 Chain R: D.123 Chain T: D.123 Ligands: UQ5.7 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.8, B:V.12, B:H.16, B:V.195, B:F.196, B:A.199, A:V.12, A:F.196, A:F.196 Salt bridges: B:H.16, A:H.16 Hydrogen bonds: A:Q.8 CDL.15: 15 residues within 4Å: Chain B: V.18, M.38, G.222, G.226, D.229, L.230 Chain C: Q.106, R.110, Y.113 Chain E: S.295, R.299 Chain M: R.488 Ligands: UQ5.7, PC7.22, CDL.28 7 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: B:D.229, B:L.230, C:Y.113 Salt bridges: C:R.110, E:R.299 Hydrogen bonds: E:S.295, E:S.295 CDL.19: 11 residues within 4Å: Chain A: G.226, D.229, L.230 Chain D: R.110, Y.113 Chain F: S.295, R.299 Chain N: L.493 Chain P: W.30 Ligands: PTY.21, PC7.23 9 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 4 interactions with chain F, 1 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: A:D.229, D:Y.113, P:W.30, N:L.493 Salt bridges: D:R.110, F:R.299 Hydrogen bonds: F:S.295, F:S.295, F:S.295 CDL.24: 18 residues within 4Å: Chain B: Y.28, F.235 Chain C: V.105 Chain E: S.286, I.287, G.290, A.293, Y.294, K.296, R.297 Chain K: I.24, T.27, F.28, N.30, A.31, T.34 Ligands: CDL.11, 3PH.16 16 PLIP interactions: 5 interactions with chain K, 8 interactions with chain E, 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: K:T.27, K:F.28, E:Y.294, E:Y.294, B:F.235, C:V.105 Hydrogen bonds: K:T.27, K:N.30, K:T.34 Water bridges: E:K.296, E:K.296, E:K.304, B:K.228 Salt bridges: E:K.296, E:R.297, E:K.304 CDL.27: 16 residues within 4Å: Chain A: Y.28, F.235 Chain F: G.290, A.293, K.296, R.297 Chain L: I.24, Q.26, T.27, F.28, N.30, A.31, T.34, F.35 Chain R: H.76 Ligands: CDL.5 11 PLIP interactions: 1 interactions with chain A, 5 interactions with chain L, 4 interactions with chain F, 1 interactions with chain R Hydrophobic interactions: A:F.235, L:I.24, L:F.28, L:F.35 Hydrogen bonds: L:N.30, L:T.34, F:R.297, R:H.76 Water bridges: F:K.296 Salt bridges: F:K.296, F:R.297 CDL.28: 13 residues within 4Å: Chain B: H.4, L.10, L.13, N.14, V.18 Chain M: Y.385, R.488, R.489, W.492, L.493, R.494 Ligands: CDL.15, PC7.22 10 PLIP interactions: 7 interactions with chain M, 3 interactions with chain B Hydrogen bonds: M:Y.385, M:L.493, M:R.494 Water bridges: M:R.488, B:M.3, B:M.3 Salt bridges: M:R.488, M:R.489, M:R.494 Hydrophobic interactions: B:L.13

7 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)(Covalent)

3PH.6: 8 residues within 4Å: Chain A: Y.94, L.251, W.273, W.277, V.330, L.331, T.334, W.335 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.94, A:Y.94, A:Y.94, A:W.273, A:W.273, A:W.277, A:V.330, A:L.331, A:T.334 3PH.12: 11 residues within 4Å: Chain B: L.238, V.239, I.242, F.246, Y.247, L.250 Chain E: I.279, C.282, S.286, I.289 Ligands: 3PH.13 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:V.239, B:I.242, B:F.246, B:Y.247, E:I.279, E:I.289 Hydrogen bonds: B:Y.247 3PH.13: 8 residues within 4Å: Chain B: Y.94, V.97, W.273, L.331, T.334, G.338, N.339 Ligands: 3PH.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.94, B:V.97, B:W.273, B:W.273, B:W.273, B:L.331 Hydrogen bonds: B:N.339 3PH.16: 9 residues within 4Å: Chain C: F.101, F.104, T.107, G.108, F.111, L.112 Chain E: F.291 Chain G: M.3 Ligands: CDL.24 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:F.104, C:T.107, C:F.111, C:L.112, E:F.291, E:F.291 3PH.25: 5 residues within 4Å: Chain K: L.46, A.47, V.51, G.55, H.65 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:V.51, K:H.65 3PH.26: 2 residues within 4Å: Chain K: L.36, F.39 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:L.36, K:F.39 3PH.31: 14 residues within 4Å: Chain A: I.112, I.115, L.193, F.196 Chain B: K.6 Chain O: S.7, Y.12, R.17 Chain R: E.45, R.105, Y.117, T.118, R.119, Y.121 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain R, 1 interactions with chain O, 2 interactions with chain B Hydrophobic interactions: A:I.115, A:L.193, A:F.196, O:Y.12 Hydrogen bonds: R:Y.117, R:T.118 Salt bridges: R:R.119, B:K.6, B:K.6

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.17: 15 residues within 4Å: Chain B: S.42, T.46, I.77, F.240, F.245 Chain C: L.119, A.120, K.123, I.124 Chain E: V.276, M.277, K.280, M.284, I.285 Chain G: D.36 10 PLIP interactions: 2 interactions with chain E, 5 interactions with chain C, 2 interactions with chain B, 1 interactions with chain G Hydrophobic interactions: E:I.285, C:A.120, C:A.120, C:K.123, C:I.124, B:T.46, B:F.240 Salt bridges: E:K.280, C:K.123 Hydrogen bonds: G:D.36 PTY.21: 15 residues within 4Å: Chain A: M.38, S.42, A.233, L.234, F.245 Chain D: A.116, L.119, K.123 Chain F: V.276, M.277, K.280, A.281, I.285 Chain H: D.36 Ligands: CDL.19 11 PLIP interactions: 3 interactions with chain D, 5 interactions with chain F, 2 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: D:A.116, D:K.123, F:A.281, F:I.285, A:A.233, A:L.234 Salt bridges: D:K.123, F:K.280 Hydrogen bonds: F:V.276 Water bridges: F:K.280, H:N.32

2 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.22: 15 residues within 4Å: Chain C: Y.103, R.110, Y.113 Chain G: F.14, S.17, Y.20, I.21, L.24 Chain M: D.466, Y.491, L.493 Chain O: Y.40, M.41 Ligands: CDL.15, CDL.28 12 PLIP interactions: 6 interactions with chain C, 1 interactions with chain O, 3 interactions with chain G, 2 interactions with chain M Hydrophobic interactions: C:R.110, C:Y.113, O:Y.40, G:I.21, G:I.21, G:L.24 Hydrogen bonds: C:R.110 Salt bridges: C:R.110, C:R.110, M:D.466 pi-Cation interactions: C:Y.103, M:Y.491 PC7.23: 14 residues within 4Å: Chain D: Y.103, R.110, Y.113 Chain H: F.14, S.17, Y.20, I.21, L.24 Chain N: D.466, Y.491, L.493 Chain P: Y.40, M.41 Ligands: CDL.19 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain H, 2 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: D:Y.113, H:I.21, H:L.24, P:Y.40 Salt bridges: D:R.110, D:R.110, N:D.466 pi-Cation interactions: D:Y.103, N:Y.491

2 x ZN: ZINC ION(Non-covalent)

ZN.29: 2 residues within 4Å: Chain M: H.103, L.214 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:H.103, M:H.103 ZN.30: 3 residues within 4Å: Chain N: H.103, H.107, E.183 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waltz, F. et al., In-cell architecture of the mitochondrial respiratory chain. Science (2025)

Release Date

2025-03-12

Peptides

Cytochrome b: AB
Cytochrome b-c1 complex subunit Rieske, mitochondrial: CD
Cytochrome c1: EF
Complex III subunit 9: GH
Cytochrome b-c1 complex subunit 6: IJ
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8: KL
MPP-Beta: MN
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10: OP
Alpha-MPP: QS
Cytochrome b-c1 complex subunit 7: RT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1A

B
1B

C
1C

D
1D

E
1E

F
1F

G
1G

H
1H

I
1I

J
1J

K
1K

L
1L

M
1M

N
1N

O
1O

P
1P

Q
1Q

S
1S

R
1R

T
1T

Membrane

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

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome c1

Complex III subunit 9

Cytochrome b-c1 complex subunit 6

Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8

MPP-Beta

Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10

Alpha-MPP

Cytochrome b-c1 complex subunit 7