SMTL ID : 8beh.1

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

3PH.1: 12 residues within 4Å: Chain A: I.30, T.33, T.34, S.37, F.38, I.41, I.101, P.460, I.461, P.462, I.465 Chain E: W.32 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.30, A:T.33, A:F.38, A:F.38, A:I.41, A:I.101, A:I.461, A:I.465, E:W.32 Hydrogen bonds: A:I.461 3PH.5: 12 residues within 4Å: Chain B: P.462, V.465, G.466, V.468, W.469, Y.473, K.475, V.476 Chain E: L.77, G.78, L.81, N.82 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:V.468, B:W.469, B:W.469, B:W.469, B:W.469, B:W.469, B:Y.473, E:L.77, E:L.77, E:L.81 Hydrogen bonds: B:Y.473, E:N.82 Salt bridges: B:K.475 3PH.7: 13 residues within 4Å: Chain A: F.295, F.558, F.559 Chain I: Y.76, E.77, L.79, A.80, W.81, S.83, G.84, G.85, F.88 Ligands: PC7.4 12 PLIP interactions: 9 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: I:E.77, I:L.79, I:A.80, I:W.81, I:W.81, I:W.81, I:F.88, I:F.88, A:F.295, A:F.558, A:F.559 Hydrogen bonds: I:E.77

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.2: 26 residues within 4Å: Chain A: L.10, S.13, S.14, G.17, F.18, H.109, R.112, C.115, Y.116, L.145, L.149 Chain B: V.371, S.372, T.379, F.382, L.391, P.392, G.393, Y.433 Chain D: R.16, S.21, M.22, T.23, G.24, G.25, P.26 15 PLIP interactions: 6 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.16, D:S.21, D:T.23, D:T.23, D:G.25, B:T.379 Water bridges: D:M.22 Hydrophobic interactions: A:L.10, A:F.18, A:L.145, A:L.149, B:L.391 Salt bridges: A:H.109, A:R.112, A:R.112

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.3: 15 residues within 4Å: Chain A: F.210, C.211, L.215, N.216, S.219, L.220, I.223, L.224, F.226, I.227, I.236, T.281, V.285, A.289 Chain B: T.416 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.210, A:L.215, A:L.220, A:I.223, A:F.226, A:I.227, A:I.236, A:T.281, A:V.285, A:A.289, B:T.416 Hydrogen bonds: A:N.216, A:N.216, A:S.219, A:T.281

1 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)

PC7.4: 19 residues within 4Å: Chain A: F.295, I.302, L.303, V.425, L.428, F.429, Y.432, V.531, V.535, F.542, Q.543, F.546, L.555, Y.556, F.559 Chain K: W.34, A.35, H.37 Ligands: 3PH.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.295, A:I.302, A:L.303, A:L.303, A:V.425, A:L.428, A:F.429, A:Y.432, A:F.546, A:L.555, A:F.559, A:F.559 Hydrogen bonds: A:Y.556 Water bridges: A:R.436, A:N.536

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Non-covalent)

8Q1.6: 16 residues within 4Å: Chain C: Q.72, S.79 Chain K: R.13, K.17, V.20, R.21, L.48, F.52, N.55, Q.56, V.58, I.64, L.67, G.71, Y.75, W.78 15 PLIP interactions: 10 interactions with chain K, 5 interactions with chain C Hydrophobic interactions: K:V.20, K:L.48, K:F.52, K:F.52, K:F.52, K:I.64, K:W.78 Hydrogen bonds: K:R.13, K:R.13, C:Q.72, C:S.79, C:S.79, C:S.79 Salt bridges: K:R.21 Water bridges: C:L.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klusch, N. et al., Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 angstrom resolution. Nat.Plants (2023)

Release Date

2023-01-11

Peptides

NADH-ubiquinone oxidoreductase chain 5: A
NADH-ubiquinone oxidoreductase chain 4: B
Acyl carrier protein 1, mitochondrial: C
Transmembrane protein: D
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein: E
At1g67350: F
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2: G
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A: H
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: I
AT2G31490 protein: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: L
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
T

D
c

E
g

F
i

G
j

H
k

I
l

J
m

K
n

L
o

M
p

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

Acyl carrier protein 1, mitochondrial

Transmembrane protein

ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein

At1g67350

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

AT2G31490 protein

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B

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