SMTL ID : 6khi.1

Supercomplex for cylic electron transport in cyanobacteria

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.1: 23 residues within 4Å: Chain A: D.6, L.7, Q.8, W.29, P.33, M.36, M.37, V.40, V.43, G.44, V.47, F.119, N.122, L.123, L.124, I.125, S.126, I.311, L.315, Y.319 Chain C: Y.21 Chain L: Y.20 Ligands: DGD.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.40, A:V.43, A:V.47, A:F.119, A:F.119, A:F.119, A:I.311, A:L.315, A:L.315 Hydrogen bonds: A:L.7, A:Q.8, A:W.29 DGD.2: 24 residues within 4Å: Chain A: I.5, D.6, L.7, M.36, I.39, G.120, Q.121, N.122, L.123, W.280, E.297, Q.303, F.306, A.307, V.308, I.311 Chain L: Y.13, L.16, A.17, Y.20, F.53, F.54, P.56 Ligands: DGD.1 22 PLIP interactions: 10 interactions with chain A, 12 interactions with chain L Hydrophobic interactions: A:I.39, A:V.308, A:I.311, L:Y.13, L:L.16, L:L.16, L:A.17, L:Y.20, L:Y.20, L:Y.20, L:Y.20, L:F.53, L:F.54, L:F.54, L:P.56 Hydrogen bonds: A:I.5, A:Q.121, A:N.122, A:W.280, A:E.297, A:E.297, A:F.306

6 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.3: 17 residues within 4Å: Chain B: Y.366, Q.367, P.370, T.373, L.374, S.377, P.388, V.433, S.472 Chain D: P.22, K.112, P.113, R.114, L.115, F.118, A.122, I.148 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:P.22, D:L.115, D:F.118, D:F.118, D:F.118, D:A.122, D:I.148, B:Y.366, B:L.374, B:L.374, B:P.388, B:P.388, B:V.433 Hydrogen bonds: D:R.114, B:Y.366 LHG.5: 7 residues within 4Å: Chain A: P.350 Chain B: I.34 Chain C: V.121, W.124, R.125 Chain I: F.3 Ligands: LHG.14 9 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 4 interactions with chain I Hydrophobic interactions: C:V.121, C:W.124, C:W.124, A:P.350, B:I.34, I:F.3, I:F.3, I:F.3, I:F.3 LHG.10: 18 residues within 4Å: Chain D: F.97, K.374, P.461, V.464, F.465, A.468, C.469 Chain F: F.24, A.28, F.29 Chain P: L.11, A.13, M.14, V.17, F.18, L.21, F.25 Ligands: BCR.7 12 PLIP interactions: 3 interactions with chain P, 7 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: P:L.11, P:V.17, P:F.18, D:F.97, D:F.97, D:V.464, D:F.465, D:A.468, F:F.24, F:A.28 Hydrogen bonds: D:K.374, D:K.374 LHG.12: 21 residues within 4Å: Chain D: Y.297, I.428, I.432, S.436, R.439 Chain F: E.173, Q.176, K.177, V.180, T.181, V.184, P.245, L.246, Y.586, E.587, F.590, I.591, C.594, R.595 Chain Q: I.9 Ligands: BCR.8 20 PLIP interactions: 6 interactions with chain D, 14 interactions with chain F Hydrophobic interactions: D:I.428, D:I.432, F:V.180, F:T.181, F:V.184, F:P.245, F:L.246, F:Y.586, F:Y.586, F:F.590, F:F.590, F:F.590 Hydrogen bonds: D:Y.297, D:S.436, D:R.439, F:E.173, F:Q.176, F:E.587 Salt bridges: D:R.439, F:R.595 LHG.13: 10 residues within 4Å: Chain F: Q.6, Y.7, W.9, V.13, L.16, Q.71, G.86, Y.87, Q.146, F.150 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:W.9, F:W.9, F:V.13, F:L.16, F:Q.71, F:F.150, F:F.150 Hydrogen bonds: F:Q.71 LHG.14: 12 residues within 4Å: Chain A: I.221, D.342, L.343, F.347 Chain C: W.124 Chain I: Q.6, I.7, Y.10, E.13, A.14, A.18 Ligands: LHG.5 13 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 9 interactions with chain I Hydrophobic interactions: A:L.343, A:F.347, C:W.124, C:W.124, I:I.7, I:I.7, I:I.7, I:Y.10, I:Y.10, I:Y.10, I:A.14, I:A.18 Hydrogen bonds: I:Q.6

3 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.4: 16 residues within 4Å: Chain A: K.26, L.27, L.30 Chain C: F.14, L.16, S.17, Y.19, E.20, F.22, L.23 Chain G: L.3, A.4, T.7, Q.8, I.51, L.52 16 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: A:L.27, A:L.30, C:F.14, C:E.20, C:F.22, C:L.23, C:L.23, G:L.3, G:T.7, G:Q.8, G:I.51, G:L.52 Salt bridges: A:K.26, A:K.26 Hydrogen bonds: C:L.16, G:Q.8 SQD.6: 22 residues within 4Å: Chain B: L.416, I.420, Y.423, K.430 Chain D: Q.163, Y.164, T.167, K.168, L.171, Y.172, G.175, V.220, V.224, P.230 Chain F: V.609, V.612, V.613, N.614, T.616, G.617, T.620, M.621 14 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: B:L.416, B:I.420, B:Y.423, B:Y.423, D:L.171, D:L.171, D:Y.172, D:V.220, D:V.224, F:V.609, F:V.612, F:T.616 Hydrogen bonds: B:Y.423 Salt bridges: B:K.430 SQD.18: 18 residues within 4Å: Chain A: L.74, L.77 Chain K: D.33, V.34, W.37 Chain L: P.63, F.64, I.65, N.66, R.68 Chain N: G.2, L.3, L.4, F.29, R.32, R.136, V.137, V.138 14 PLIP interactions: 2 interactions with chain A, 3 interactions with chain N, 4 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: A:L.74, A:L.77, N:L.4, K:D.33, K:V.34, K:W.37, K:W.37, L:P.63, L:P.63 Hydrogen bonds: N:V.138, L:N.66 Salt bridges: N:R.32, L:R.68, L:R.68

2 x BCR: BETA-CAROTENE(Non-covalent)

BCR.7: 20 residues within 4Å: Chain D: L.93, L.94, F.97, M.378, A.381, A.468, L.471, V.472, I.475, G.476, I.477, L.483, L.484 Chain F: L.20, I.27 Chain P: I.10, L.11, M.14 Ligands: LMG.9, LHG.10 13 PLIP interactions: 10 interactions with chain D, 1 interactions with chain P, 2 interactions with chain F Hydrophobic interactions: D:L.93, D:L.94, D:F.97, D:A.381, D:A.468, D:L.471, D:I.475, D:I.475, D:I.477, D:L.483, P:L.11, F:L.20, F:I.27 BCR.8: 14 residues within 4Å: Chain D: V.287, I.290, Y.291, F.421, L.422 Chain F: F.187, L.235, V.238, P.245, T.297 Chain Q: I.28, F.31, I.32 Ligands: LHG.12 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 1 interactions with chain Q Hydrophobic interactions: D:I.290, D:Y.291, D:L.422, F:V.238, Q:F.31

2 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.9: 16 residues within 4Å: Chain D: K.373, F.376, A.377, T.380, M.392 Chain F: A.19, G.23, L.26, P.119, R.123, Y.127, L.130, M.156, L.160, Y.166 Ligands: BCR.7 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.19, F:L.26, F:L.130, F:L.160 Hydrogen bonds: F:R.123, F:Y.127, F:Y.166, F:Y.166 Salt bridges: F:R.123, F:R.123, D:K.373 LMG.11: 16 residues within 4Å: Chain F: T.307, I.310, T.311, N.313, L.441, F.444, R.448, V.550, Y.555, P.562, Q.563, L.572, Y.573, F.575, S.576, W.580 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:T.307, F:I.310, F:L.441, F:F.444, F:F.444, F:V.550, F:L.572, F:L.572, F:W.580 Hydrogen bonds: F:I.310, F:N.313, F:R.448, F:Y.555, F:Y.555, F:S.576

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

SF4.15: 11 residues within 4Å: Chain I: C.73, P.74, P.78, I.98, C.103, I.104, F.105, C.106, A.107, N.108, C.109 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.73, I:C.103, I:C.106, I:C.109 SF4.16: 12 residues within 4Å: Chain I: C.63, I.64, A.65, C.66, V.68, C.69, Y.96, Y.112, C.113, T.115, C.117, L.118 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.63, I:C.66, I:C.69, I:C.113 SF4.17: 13 residues within 4Å: Chain H: R.69, I.154 Chain K: A.51, C.52, C.53, G.88, T.89, G.115, A.116, C.117, M.123, C.148, P.149 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.52, K:C.53, K:C.117, K:C.148

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

FES.19: 11 residues within 4Å: Chain T: F.39, S.40, C.41, R.42, G.44, A.45, C.46, S.47, C.49, L.77, C.79 4 PLIP interactions: 4 interactions with chain T, Metal complexes: T:C.41, T:C.46, T:C.49, T:C.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase. Nat Commun (2020)

Release Date

2020-02-12

Peptides

NAD(P)H-quinone oxidoreductase subunit 1: A
NAD(P)H-quinone oxidoreductase subunit 2: B
NAD(P)H-quinone oxidoreductase subunit 3: C
NAD(P)H-quinone oxidoreductase chain 4 1: D
NAD(P)H-quinone oxidoreductase subunit 4L: E
NADH dehydrogenase subunit 5: F
NADH-quinone oxidoreductase subunit J: G
NAD(P)H-quinone oxidoreductase subunit H: H
NAD(P)H-quinone oxidoreductase subunit I: I
NAD(P)H-quinone oxidoreductase subunit J: J
NAD(P)H-quinone oxidoreductase subunit K: K
NAD(P)H-quinone oxidoreductase subunit L: L
NAD(P)H-quinone oxidoreductase subunit M: M
NAD(P)H-quinone oxidoreductase subunit N: N
NAD(P)H-quinone oxidoreductase subunit O: O
proton-translocating NADH-quinone dehydrogenase subunit P: P
proton-translocating NADH-quinone dehydrogenase subunit Q: Q
Tlr0636 protein: R
Tlr0472 protein: S
Ferredoxin-1: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
S

S
V

T
1

Membrane

We predict this structure to be a membrane protein.
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NAD(P)H-quinone oxidoreductase subunit 1

NAD(P)H-quinone oxidoreductase subunit 2

NAD(P)H-quinone oxidoreductase subunit 3

NAD(P)H-quinone oxidoreductase chain 4 1

NAD(P)H-quinone oxidoreductase subunit 4L

NADH dehydrogenase subunit 5

NADH-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit H

NAD(P)H-quinone oxidoreductase subunit I

NAD(P)H-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit K

NAD(P)H-quinone oxidoreductase subunit L

NAD(P)H-quinone oxidoreductase subunit M

NAD(P)H-quinone oxidoreductase subunit N

NAD(P)H-quinone oxidoreductase subunit O

proton-translocating NADH-quinone dehydrogenase subunit P

proton-translocating NADH-quinone dehydrogenase subunit Q

Tlr0636 protein

Tlr0472 protein

Ferredoxin-1

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