SMTL ID : 7aqr.1

Cryo-EM structure of Arabidopsis thaliana Complex-I (peripheral arm)

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-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: A.92, C.93, C.94, G.129, T.130, G.156, S.157, C.158, G.187, C.188, P.189 Chain C: R.69, H.154 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.93, A:C.94, A:C.158, A:C.188 SF4.4: 13 residues within 4Å: Chain E: I.228, P.246, S.401, C.402, G.403, Q.404, C.405, C.408, T.446, I.447, C.448, L.450, G.451 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.402, E:C.405, E:C.408, E:C.448 SF4.6: 11 residues within 4Å: Chain C: M.306 Chain F: H.166, D.169, C.170, C.173, Q.175, G.176, C.179, L.181, V.270, G.271 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:D.169 Metal complexes: F:H.166, F:C.170, F:C.173, F:C.179 SF4.7: 11 residues within 4Å: Chain F: M.215, C.218, I.219, C.221, T.222, C.224, I.248, C.268, V.270, A.272, L.273 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.218, F:C.221, F:C.224, F:C.268 SF4.8: 12 residues within 4Å: Chain G: H.111, C.133, P.134, I.138, C.162, I.163, Y.164, C.165, G.166, F.167, C.168, E.179 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:E.179 Metal complexes: G:C.133, G:C.162, G:C.165, G:C.168 SF4.9: 12 residues within 4Å: Chain G: C.123, I.124, A.125, C.126, K.127, C.129, I.140, Y.155, C.172, V.174, A.176, I.177 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.123, G:C.126, G:C.129, G:C.172

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

FES.2: 7 residues within 4Å: Chain D: G.131, T.132, C.135, M.169, C.171, C.175, M.180 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.135, D:C.171, D:C.175 FES.5: 9 residues within 4Å: Chain F: R.104, C.106, Y.107, G.115, N.116, C.117, R.118, C.120, C.134 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.106, F:C.117, F:C.120, F:C.134

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain E: G.110, R.111, G.112, A.114, K.121, N.139, D.141, E.142, S.143, Y.227, G.230, E.231, E.232, V.265, T.266, N.267, T.270, A.449, L.450 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.227, E:E.231, E:E.231, E:A.449, E:L.450 Hydrogen bonds: E:G.112, E:N.139, E:S.143, E:G.230, E:E.232, E:N.267, E:N.267 Salt bridges: E:K.121

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.10: 25 residues within 4Å: Chain A: K.218 Chain H: G.75, A.76, T.77, G.78, F.79, L.80, R.100, P.125, L.144, I.145, G.146, R.147, F.154, A.159, I.163, V.183, S.184, C.185, K.200, P.219, A.220, T.221, M.222, R.228 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:G.75, H:T.77, H:T.77, H:T.77, H:F.79, H:L.80, H:R.100, H:L.144, H:G.146, H:R.147, H:K.200, H:M.222 Salt bridges: H:R.100, H:R.147, H:R.147, H:R.228, H:R.228, A:K.218 pi-Cation interactions: H:R.100

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain J: C.72, H.82, C.97, C.100 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.72, J:H.82, J:C.97, J:C.100

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

8Q1.12: 20 residues within 4Å: Chain L: D.82, S.83, L.84 Chain N: R.23, V.26, F.27, F.29, I.40, I.59, Q.62, I.63, N.66, A.67, I.69, I.75, L.78, G.82, L.86, I.89, Y.103 14 PLIP interactions: 11 interactions with chain N, 3 interactions with chain L Hydrophobic interactions: N:F.29, N:I.40, N:I.59, N:Q.62, N:A.67, N:I.75, N:L.86, N:L.86, N:Y.103, L:L.84 Hydrogen bonds: N:N.66, L:D.82, L:S.83 Salt bridges: N:R.23

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 dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3: B
NADH dehydrogenase subunit 7: C
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: E
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial: F
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: I
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: K
Acyl carrier protein 2, mitochondrial: L
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: O
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: P
Furry: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
G

G
I

H
P

I
Q

J
R

K
S

L
U

M
V

N
W

O
Z

P
q

Q
r

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

NADH dehydrogenase subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein 2, mitochondrial

Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

Furry

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