SMTL ID : 8bee.1

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 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 SF4.2: 11 residues within 4Å: Chain D: H.111, C.133, I.138, C.162, I.163, Y.164, C.165, G.166, F.167, C.168, E.179 6 PLIP interactions: 6 interactions with chain D, Salt bridges: D:E.179 Metal complexes: D:H.111, D:C.133, D:C.162, D:C.165, D:C.168 SF4.3: 14 residues within 4Å: Chain D: C.123, I.124, A.125, C.126, K.127, L.128, C.129, I.140, Y.155, C.172, P.173, V.174, A.176, I.177 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.123, D:C.126, D:C.129, D:C.172

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

NDP.4: 24 residues within 4Å: Chain A: K.218 Chain E: 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, I.163, V.183, S.184, C.185, K.200, P.219, A.220, T.221, M.222, R.228 35 PLIP interactions: 34 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.75, E:T.77, E:T.77, E:T.77, E:F.79, E:L.80, E:L.144, E:G.146, E:K.200, E:M.222, E:R.228 Water bridges: E:G.78, E:G.81, E:R.100, E:R.100, E:R.100, E:R.100, E:G.101, E:S.105, E:R.147, E:R.147, E:R.147, E:E.148, E:E.148, E:M.222, E:R.228, E:R.228 Salt bridges: E:R.100, E:R.147, E:R.147, E:R.228, E:R.228, A:K.218 pi-Cation interactions: E:R.100, E:R.100

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

8Q1.5: 17 residues within 4Å: Chain F: D.82, S.83, L.84 Chain H: R.23, V.26, F.29, I.59, Q.62, I.63, R.64, N.66, A.67, I.69, I.75, L.86, I.89, Y.103 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: H:I.59, H:Q.62, H:I.75, H:L.86, H:I.89 Hydrogen bonds: H:R.23, H:N.66, H:A.67, F:S.83, F:L.84

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 dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3: B
NADH dehydrogenase subunit 7: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: E
Acyl carrier protein 2, mitochondrial: F
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: I
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
I

E
P

F
U

G
V

H
W

I
Z

J
q

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

NADH dehydrogenase subunit 7

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

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

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

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