SMTL ID : 8b6g.1

Cryo-EM structure of succinate dehydrogenase complex (complex-II) in respiratory supercomplex of Tetrahymena thermophila

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

7 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 50 residues within 4Å: Chain B: A.2, R.3, L.4, W.5, W.6 Chain I: G.40, V.41, I.44, F.45, F.48 Chain L: Y.28, V.32, G.33, L.36, Y.37, I.40 Chain M: I.25, R.26, I.29, V.30, L.32, N.33, T.34, W.35, I.36, V.37, G.38, Y.39, A.40, V.41, S.42, Y.45, F.46 Chain N: V.17, F.20, T.21, A.24, T.25, C.27, L.30 Chain O: M.1, F.2, E.4, L.5, I.8, F.9 Ligands: 3PE.14, CDL.17, CDL.18, 3PE.19 28 PLIP interactions: 4 interactions with chain I, 9 interactions with chain M, 1 interactions with chain N, 7 interactions with chain B, 3 interactions with chain O, 4 interactions with chain L Hydrophobic interactions: I:V.41, I:I.44, I:F.48, I:F.48, M:L.32, M:N.33, M:W.35, M:I.36, M:I.36, M:V.37, M:Y.39, M:Y.39, N:F.20, B:W.5, B:W.5, B:W.6, O:E.4, O:L.5, O:L.5, L:Y.28, L:V.32, L:L.36, L:Y.37 Salt bridges: M:R.26 Hydrogen bonds: B:R.3, B:W.5, B:W.5, B:W.6 CDL.8: 27 residues within 4Å: Chain B: I.18, S.19, N.24, L.27, F.28, L.31 Chain H: F.11, R.15, K.49, E.52, F.55, Y.56 Chain K: Y.35, A.36, Y.38, A.39, Y.41, L.42, A.43, W.46, A.47, P.48 Chain O: I.40 Ligands: CDL.9, CDL.11, CDL.13, 3PE.19 14 PLIP interactions: 5 interactions with chain H, 3 interactions with chain B, 5 interactions with chain K, 1 interactions with chain O Hydrogen bonds: H:E.52, H:E.52, H:Y.56, B:S.19, B:N.24, K:Y.38 Salt bridges: H:R.15, H:K.49 Hydrophobic interactions: B:F.28, K:Y.38, K:A.39, K:L.42, K:L.42, O:I.40 CDL.9: 19 residues within 4Å: Chain H: V.4, F.7, K.8, F.11, R.15, R.58, N.62, W.63, S.64 Chain J: L.322 Chain K: P.28, A.31, T.32, Y.35, A.36, A.39 Ligands: CDL.8, CDL.11, CDL.13 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain K Hydrophobic interactions: H:F.7, K:Y.35 Hydrogen bonds: H:N.62, H:W.63, H:S.64, K:Y.35 Salt bridges: H:K.8, H:K.8, H:R.58 CDL.11: 26 residues within 4Å: Chain H: H.92, A.93, Q.96 Chain I: F.27, R.30, T.31, R.34, N.35, F.38 Chain K: S.20, F.23, R.24, F.29, T.32, I.33, A.36, T.37, N.40 Chain O: K.20, S.22, N.23, F.26, L.30 Ligands: CDL.8, CDL.9, CDL.13 14 PLIP interactions: 6 interactions with chain K, 5 interactions with chain I, 2 interactions with chain O, 1 interactions with chain H Hydrophobic interactions: K:T.32, K:I.33, K:I.33, K:A.36, I:F.38, O:F.26, O:F.26, H:Q.96 Hydrogen bonds: K:S.20, K:R.24, I:N.35 Salt bridges: I:R.30, I:R.34, I:R.34 CDL.13: 40 residues within 4Å: Chain B: P.10, S.11, Y.14, R.23, E.25, F.28, T.29, L.31, G.32, A.35 Chain K: A.36, A.39, N.40, A.43, Q.44, A.47, P.48, R.49, V.50, S.51, V.72, Y.73, I.76, G.77, L.80 Chain N: A.9, H.12, Y.13 Chain O: F.26, N.29, L.30, Y.32, T.33, A.36, Y.37, I.40 Ligands: CDL.8, CDL.9, CDL.11, 3PE.19 17 PLIP interactions: 11 interactions with chain K, 2 interactions with chain B, 2 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: K:N.40, K:A.43, K:Y.73, K:Y.73, K:Y.73, K:I.76, B:L.31, O:T.33, O:I.40 Hydrogen bonds: K:V.50, K:S.51, B:S.11 Salt bridges: K:R.49, K:R.49, K:R.49, N:H.12, N:H.12 CDL.17: 27 residues within 4Å: Chain L: S.19, P.22, K.23, L.26, P.29, I.30, G.33, V.34, Y.37 Chain M: T.34, W.35, G.38, Y.39, S.42, R.43, Y.45, F.46, L.49 Chain N: L.30, D.31, K.34, Y.35 Ligands: CDL.1, 3PE.14, PC1.15, UQ8.16, CDL.18 9 PLIP interactions: 3 interactions with chain L, 3 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: L:K.23, L:K.23, L:L.26 Hydrogen bonds: M:Y.39, M:S.42, M:S.42 Salt bridges: N:K.34, N:K.34, N:K.34 CDL.18: 31 residues within 4Å: Chain G: P.208, S.210, F.211, L.213, G.214, V.217, L.218, A.221, L.224 Chain H: R.114, A.117, S.119, N.120, F.121, H.122, N.123 Chain I: F.33, Y.36, Y.37, G.40, V.41, I.44 Chain M: Y.45 Chain O: Y.13, I.14, T.15 Ligands: CDL.1, 3PE.14, PC1.15, CDL.17, 3PE.19 23 PLIP interactions: 7 interactions with chain I, 6 interactions with chain H, 5 interactions with chain O, 5 interactions with chain G Hydrophobic interactions: I:Y.36, I:Y.36, I:Y.37, I:V.41, I:I.44, H:F.121, H:F.121, O:Y.13, G:V.217, G:V.217, G:L.218, G:A.221 Hydrogen bonds: I:Y.36, I:Y.37, H:R.114, O:Y.12, O:I.14, O:T.15, O:T.15, G:S.210 Salt bridges: H:R.114, H:H.122, H:H.122

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain D: Y.396, N.397, M.398, G.399, E.429, A.431, C.432, H.436 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:N.397, D:G.399, D:E.429 CA.7: 4 residues within 4Å: Chain F: I.248, D.250, D.253, T.256 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:I.248, F:D.250, F:D.253, F:T.256

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 45 residues within 4Å: Chain D: V.54, G.55, A.56, G.57, G.58, A.59, I.77, T.78, K.79, L.80, P.82, S.85, H.86, T.87, A.89, A.90, Q.91, G.92, G.93, F.160, Y.206, F.207, V.208, A.244, G.245, T.255, A.256, A.257, T.259, C.260, D.263, L.294, R.328, H.395, Y.396, G.428, E.429, N.430, R.440, A.443, N.444, S.445, L.446, I.449 Chain F: E.124 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:L.294 Hydrogen bonds: D:A.56, D:G.57, D:G.58, D:A.59, D:I.77, D:T.78, D:K.79, D:K.79, D:L.80, D:H.86, D:T.87, D:T.87, D:T.87, D:Q.91, D:G.92, D:V.208, D:V.208, D:G.245, D:D.263, D:E.429, D:E.429, D:E.429, D:R.440, D:A.443, D:S.445, D:S.445, D:S.445, D:L.446 pi-Stacking: D:H.395 pi-Cation interactions: D:R.328

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

FES.4: 14 residues within 4Å: Chain F: L.102, R.120, S.121, C.122, R.123, E.124, G.125, I.126, C.127, G.128, S.129, C.130, L.140, C.142 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.122, F:C.127, F:C.130, F:C.142

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.5: 14 residues within 4Å: Chain F: C.215, V.216, L.217, C.218, A.219, A.220, C.221, A.239, Q.242, C.282, P.283, K.284, L.286, P.288 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.215, F:C.218, F:C.221, F:C.282

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.6: 14 residues within 4Å: Chain F: C.225, P.226, S.227, Y.235, P.238, C.272, Q.273, Q.274, I.275, G.276, M.277, C.278, Q.289, L.292 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.225, F:C.272, F:C.278

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

3PE.10: 26 residues within 4Å: Chain G: F.198, F.201, F.205, N.206, L.207, P.208, F.211, L.215, L.218, V.222 Chain H: E.111, R.114, I.131 Chain I: K.25, V.28, T.29, W.32, F.33, N.35, Y.36, V.39 Chain K: M.1, F.9, F.12, V.13, L.16 10 PLIP interactions: 3 interactions with chain G, 1 interactions with chain K, 1 interactions with chain H, 5 interactions with chain I Hydrophobic interactions: G:F.201, G:F.211, G:L.215, K:F.12, I:W.32, I:W.32, I:W.32, I:W.32, I:W.32 Salt bridges: H:R.114 3PE.14: 23 residues within 4Å: Chain G: R.112, N.182, L.185, L.186, W.187, P.188, L.213, F.216, V.217, T.220, L.224, A.225, W.228 Chain I: I.44 Chain M: V.41, Y.44, Y.45, S.48, L.49, R.50 Ligands: CDL.1, CDL.17, CDL.18 13 PLIP interactions: 5 interactions with chain M, 8 interactions with chain G Hydrophobic interactions: M:Y.44, M:Y.45, M:Y.45, G:L.185, G:W.187, G:F.216, G:L.224, G:W.228, G:W.228 Hydrogen bonds: M:R.50, G:L.186, G:W.228 Salt bridges: M:R.50 3PE.19: 33 residues within 4Å: Chain B: T.7, D.9, P.10, S.11 Chain I: Y.37, V.41, F.42, F.45 Chain K: I.76, L.80 Chain N: H.12, Y.13, A.15, A.16, V.17, F.20 Chain O: M.1, F.2, L.5, I.6, F.9, Y.13, F.16, L.27, S.31, Y.32, I.35, A.36, L.39 Ligands: CDL.1, CDL.8, CDL.13, CDL.18 16 PLIP interactions: 3 interactions with chain I, 10 interactions with chain O, 1 interactions with chain N, 1 interactions with chain B, 1 interactions with chain K Hydrophobic interactions: I:V.41, I:V.41, I:F.45, O:F.2, O:F.2, O:L.5, O:F.9, O:F.9, O:F.9, O:Y.13, O:I.35, N:H.12, K:I.76 Hydrogen bonds: O:M.1, O:F.2, B:D.9

1 x HEC: HEME C(Covalent)

HEC.12: 16 residues within 4Å: Chain J: K.37, Y.39, Y.40, R.43, E.164, T.167, R.168, K.173, H.260, H.262, Y.263, I.311, H.317, W.318, H.320, C.321 11 PLIP interactions: 11 interactions with chain J, Hydrophobic interactions: J:Y.39, J:I.311 Hydrogen bonds: J:Y.39 Salt bridges: J:R.43, J:R.168, J:H.260, J:H.262, J:H.262 pi-Cation interactions: J:H.317, J:H.320 Metal complexes: J:H.317

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.15: 24 residues within 4Å: Chain F: H.161, W.229, W.230, H.231, P.232 Chain H: Y.109, S.113, V.116, A.117, T.118, S.119 Chain L: W.6, V.13, F.18 Chain M: Y.6, Y.10, F.11 Chain O: Y.12, Y.13, I.14, R.17 Ligands: UQ8.16, CDL.17, CDL.18 7 PLIP interactions: 3 interactions with chain H, 1 interactions with chain F, 2 interactions with chain L, 1 interactions with chain M Hydrogen bonds: H:T.118, H:T.118, H:S.119, M:Y.10 Salt bridges: F:H.161 Hydrophobic interactions: L:W.6, L:F.18

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.16: 24 residues within 4Å: Chain B: A.2 Chain F: P.226, S.227, W.229, W.230, Q.273, I.275 Chain L: F.12, V.13, M.17, A.21, P.22, I.25, L.26 Chain M: Y.10, F.19, S.22, F.23, R.26, L.27 Chain O: T.11, Y.12 Ligands: PC1.15, CDL.17 11 PLIP interactions: 2 interactions with chain L, 3 interactions with chain F, 6 interactions with chain M Hydrophobic interactions: L:V.13, L:A.21, F:P.226, F:W.230, M:F.19, M:F.23, M:F.23, M:F.23 Hydrogen bonds: F:W.230, M:S.22, M:R.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muhleip, A. et al., Structural basis of mitochondrial membrane bending by the I-II-III 2 -IV 2 supercomplex. Nature (2023)

Release Date

2023-03-29

Peptides

Diphthamide synthesis protein: A
Transmembrane protein, putative: B
Transposase: C
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: D
DUF4885 domain-containing protein: E
Succinate dehydrogenase (quinone): F
Transmembrane protein, putative: G
SDHTT3: H
Transmembrane protein, putative: I
NmrA domain-containing protein: J
Transmembrane protein, putative: K
Transmembrane protein, putative: L
Cytochrome b-c1 complex subunit 8: M
SDHTT11: N
SDHD: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
CH

B
CM

C
CL

D
CA

E
CI

F
CB

G
CF

H
CG

I
CK

J
CE

K
CJ

L
CN

M
CC

N
CO

O
CD

Membrane

We predict this structure to be a membrane protein.
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Diphthamide synthesis protein

Transmembrane protein, putative

Transposase

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

DUF4885 domain-containing protein

Succinate dehydrogenase (quinone)

Transmembrane protein, putative

SDHTT3

Transmembrane protein, putative

NmrA domain-containing protein

Transmembrane protein, putative

Transmembrane protein, putative

Cytochrome b-c1 complex subunit 8

SDHTT11

SDHD

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