SMTL ID : 7aqw.1

Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 12 residues within 4Å: Chain B: I.461, L.464, V.465, V.468, W.469, V.472, Y.473, K.475 Chain E: L.77, G.78, L.81, N.82 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain B Hydrophobic interactions: E:L.77, B:I.461, B:V.465, B:V.468, B:W.469, B:W.469, B:V.472, B:Y.473 Hydrogen bonds: E:N.82, B:Y.473 Salt bridges: B:K.475

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)

PC7.2: 27 residues within 4Å: Chain A: L.10, S.13, S.14, G.17, F.18, H.109, R.112, C.115, Y.116, I.119, F.122, F.123, L.145, L.149 Chain B: V.371, S.372, S.378, T.379, F.382, F.383, Y.433 Chain D: R.16, S.21, M.22, T.23, G.25, P.26 18 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:V.371, B:T.379, B:F.382, B:F.382, B:F.382, B:F.383, A:L.10, A:F.18, A:F.18, A:F.122, A:F.123, A:L.145, A:L.149 Salt bridges: A:H.109, A:R.112 Hydrogen bonds: D:S.21, D:T.23, D:G.25

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

8Q1.3: 17 residues within 4Å: Chain C: S.79 Chain K: K.17, V.20, R.21, L.23, A.27, D.30, L.48, K.51, F.52, N.55, Q.56, V.58, I.64, G.71, Y.75, W.78 15 PLIP interactions: 13 interactions with chain K, 2 interactions with chain C Hydrophobic interactions: K:K.17, K:V.20, K:L.23, K:A.27, K:L.48, K:K.51, K:F.52, K:F.52, K:I.64, K:Y.75, K:W.78 Hydrogen bonds: K:N.55, C:S.79, C:S.79 Salt bridges: K:K.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klusch, N. et al., A ferredoxin bridge connects the two arms of plant mitochondrial complex I. Plant Cell (2021)

Release Date

2021-12-08

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
P1: 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
B15 -- 1 beta subcomplex subunit 4: 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

P1

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

B15 -- 1 beta subcomplex subunit 4

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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