SMTL ID : 8bed.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 7 residues within 4Å: Chain A: G.131, C.135, S.140, M.169, C.171, C.175, M.180 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.135, A:C.171, A:C.175 FES.4: 9 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.106, C:C.117, C:C.120, C:C.134

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain B: G.110, R.111, G.112, K.121, N.139, D.141, E.142, Y.227, G.230, E.231, E.232, V.265, T.266, N.267, T.270, A.449, L.450 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.227, B:E.231, B:E.231, B:A.449, B:L.450 Hydrogen bonds: B:R.111, B:G.112, B:N.139, B:S.143, B:G.230, B:E.232, B:T.266, B:N.267, B:N.267 Water bridges: B:G.115, B:G.115, B:S.118, B:K.121, B:D.141, B:D.141, B:E.144, B:D.150, B:G.230, B:T.266 Salt bridges: B:K.121

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

SF4.3: 13 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.402, B:C.405, B:C.408, B:C.448 SF4.5: 11 residues within 4Å: Chain C: H.166, D.169, C.170, C.173, Q.175, G.176, C.179, L.181, Q.182, V.270, G.271 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.169 Metal complexes: C:H.166, C:C.170, C:C.173, C:C.179 SF4.6: 12 residues within 4Å: Chain C: M.215, C.218, I.219, Q.220, C.221, T.222, C.224, I.248, C.268, V.270, A.272, L.273 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.218, C:C.221, C:C.224, C:C.268

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain F: C.72, G.74, H.82, C.97, C.100 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.72, F:H.82, F:C.97, F:C.100

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] flavoprotein 2, mitochondrial: A
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial: D
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: E
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: F
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
I

E
Q

F
R

G
S

H
W

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] iron-sulfur protein 4, mitochondrial

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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