SMTL ID : 7wff.1

Subcomplexes B,M and L in the Cylic electron transfer supercomplex NDH-PSI from Arabidopsis

Coordinates

PDB Format

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

2 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.1: 18 residues within 4Å: Chain B: L.442, Y.445, K.452 Chain D: L.167, Y.168, T.171, K.172, L.175, Y.176 Chain F: T.698, N.699, G.702, S.705, F.706 Chain H: T.185, D.186, G.189, L.190 11 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: D:L.175, D:L.175, D:Y.176, B:L.442, B:Y.445 Hydrogen bonds: D:Y.168, D:T.171, B:Y.445, H:D.186, H:D.186 Salt bridges: B:K.452 LHG.2: 19 residues within 4Å: Chain D: P.378, F.381, T.382, I.386, G.396, M.397, I.479 Chain F: G.23, L.26, K.34, Q.119, G.120, R.123, Y.127, F.130, M.156, L.160, F.166 Chain L: D.83 13 PLIP interactions: 9 interactions with chain F, 1 interactions with chain L, 3 interactions with chain D Hydrophobic interactions: F:L.26, F:R.123, F:F.130, F:L.160, D:I.386, D:I.479 Hydrogen bonds: F:R.123, F:Y.127, L:D.83, D:T.382 Salt bridges: F:K.34, F:R.123, F:R.123

1 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.3: 12 residues within 4Å: Chain D: K.379, P.465, L.468, I.472 Chain F: L.28, F.29, P.30 Chain K: Y.108, F.109 Chain L: D.105, I.106, A.108 11 PLIP interactions: 3 interactions with chain D, 3 interactions with chain F, 4 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: D:I.472, F:L.28, F:F.29, K:Y.108, K:F.109, K:F.109, L:I.106 Hydrogen bonds: D:K.379, F:L.28, K:Y.108 Salt bridges: D:K.379

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

FES.4: 10 residues within 4Å: Chain J: Y.110, C.120, A.121, G.122, G.124, C.126, T.128, C.129, L.160, C.162 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.120, J:C.126, J:C.129, J:C.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, X. et al., Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. Mol Plant (2022)

Release Date

2022-03-16

Peptides

NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic: A
NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic: B
NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic: C
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic: D
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic: E
NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic: F
NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic: G
Photosynthetic NDH subunit of subcomplex B 1, chloroplastic: H
Photosynthetic NDH subunit of subcomplex B 2, chloroplastic: I
Photosynthetic NDH subunit of subcomplex B 3, chloroplastic: J
NDH dependent flow 6: K
Photosynthetic NDH subunit of subcomplex B 5, chloroplastic: L
Photosynthetic NDH subunit of lumenal location 1, chloroplastic: M
Photosynthetic NDH subunit of lumenal location 2, chloroplastic: N
Photosynthetic NDH subunit of lumenal location 3, chloroplastic: O
Photosynthetic NDH subunit of lumenal location 4, chloroplastic: P
Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
a

I
b

J
c

K
d

L
e

M
f

N
g

O
h

P
i

Q
j

Membrane

We predict this structure to be a membrane protein.
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NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic

NAD(P)H-quinone oxidoreductase chain 4, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic

NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic

Photosynthetic NDH subunit of subcomplex B 1, chloroplastic

Photosynthetic NDH subunit of subcomplex B 2, chloroplastic

Photosynthetic NDH subunit of subcomplex B 3, chloroplastic

NDH dependent flow 6

Photosynthetic NDH subunit of subcomplex B 5, chloroplastic

Photosynthetic NDH subunit of lumenal location 1, chloroplastic

Photosynthetic NDH subunit of lumenal location 2, chloroplastic

Photosynthetic NDH subunit of lumenal location 3, chloroplastic

Photosynthetic NDH subunit of lumenal location 4, chloroplastic

Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic

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