SMTL ID : 7aqq.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.1: 12 residues within 4Å: Chain B: L.14, P.15, L.17, L.18, A.21, V.24, P.51, L.58, F.225, A.226, F.229, L.230 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.15, B:L.18, B:P.51, B:L.58, B:A.226, B:F.229, B:L.230, B:L.230 pi-Stacking: B:F.229

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 15 residues within 4Å: Chain B: F.184, P.185, V.188, F.191, F.275, F.287, Y.290, L.298, V.302, F.303, L.306, W.310 Chain J: V.53 Chain L: P.15, V.16 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain J Hydrophobic interactions: B:F.184, B:P.185, B:V.188, B:F.191, B:F.275, B:F.287, B:W.310, B:W.310, J:V.53 PTY.4: 19 residues within 4Å: Chain G: W.56, L.102, A.105, G.106, S.109, M.357, R.463, N.464, L.467, M.471, F.475 Chain M: T.16, Q.17, E.34, G.38, G.42 Ligands: LMN.3, PGT.8, PSF.9 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.102, G:A.105, G:L.467 Hydrogen bonds: G:N.464, G:N.464 Salt bridges: G:R.463

1 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.3: 18 residues within 4Å: Chain F: R.73, E.78 Chain G: L.478, L.481, Y.482 Chain M: I.3, S.4, A.5, V.8, L.12, G.42, F.45, A.46, L.49, V.50, V.54, K.57 Ligands: PTY.4 14 PLIP interactions: 3 interactions with chain G, 9 interactions with chain M, 2 interactions with chain F Hydrophobic interactions: G:L.478, G:L.481, M:A.5, M:V.8, M:L.12, M:L.12, M:F.45, M:A.46, M:L.49, M:V.50 Hydrogen bonds: G:Y.482, M:K.57, F:R.73 Salt bridges: F:R.73

1 x FE: FE (III) ION(Non-covalent)

FE.5: 4 residues within 4Å: Chain H: H.83, C.91, C.95, C.135 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.83, H:C.91, H:C.95, H:C.135

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)

PC7.6: 15 residues within 4Å: Chain G: I.31, I.34, H.35, F.39 Chain O: V.45, G.59, P.60, M.62, V.63, T.64, G.66, L.67, L.70 Chain R: N.81, Y.84 11 PLIP interactions: 5 interactions with chain G, 2 interactions with chain R, 4 interactions with chain O Hydrophobic interactions: G:I.31, G:I.34, G:I.34, G:F.39, G:F.39, R:Y.84, O:V.45, O:V.63, O:L.70 Hydrogen bonds: R:N.81, O:G.59

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain T: H.107, H.135 Chain U: Q.101, H.130, Y.207 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain U Metal complexes: T:H.107, T:H.135, U:H.130, U:Y.207

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.8: 8 residues within 4Å: Chain G: W.56 Chain O: L.50, S.51, K.54 Chain T: K.233 Ligands: PTY.4, PSF.9, T7X.10 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain G Hydrophobic interactions: O:L.50, G:W.56

1 x PSF: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE(Non-covalent)

PSF.9: 10 residues within 4Å: Chain G: R.463 Chain M: W.33, E.34 Chain S: Y.238 Chain U: L.22, R.24, R.28 Ligands: PTY.4, PGT.8, T7X.10 6 PLIP interactions: 5 interactions with chain U, 1 interactions with chain G Hydrophobic interactions: U:L.22 Hydrogen bonds: U:R.24, U:R.28 Salt bridges: U:R.24, U:R.28, G:R.463

1 x T7X: Phosphatidylinositol(Non-covalent)

T7X.10: 16 residues within 4Å: Chain O: T.46, Y.49, L.50, I.53 Chain R: R.82, A.85, G.89, V.90 Chain T: V.11, I.15, T.18 Chain U: L.22, L.25, R.28 Ligands: PGT.8, PSF.9 9 PLIP interactions: 5 interactions with chain U, 1 interactions with chain O, 1 interactions with chain R, 2 interactions with chain T Hydrophobic interactions: U:L.22, U:L.22, U:L.25, O:T.46, R:V.90, T:V.11, T:I.15 Hydrogen bonds: U:R.28, U:R.28

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 3: A
NADH-ubiquinone oxidoreductase chain 1: B
NADH-ubiquinone oxidoreductase chain 6: C
NADH dehydrogenase subunit 4L: D
NADH-ubiquinone oxidoreductase chain 5: E
NADH-ubiquinone oxidoreductase chain 4: F
NADH-ubiquinone oxidoreductase chain 2: G
AT3G07480.1: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: J
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: K
At2g46540/F11C10.23: L
Excitatory amino acid transporter: M
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B: N
At4g16450: O
P1: P
unknown: Q
Uncharacterized protein At2g27730, mitochondrial: R
Gamma carbonic anhydrase-like 2, mitochondrial: S
Gamma carbonic anhydrase 2, mitochondrial: T
Gamma carbonic anhydrase 1, mitochondrial: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
J

D
K

E
L

F
M

G
N

H
O

I
X

J
Z

K
a

L
b

M
d

N
e

O
f

P
i

Q
u

R
v

S
x

T
y

U
z

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase subunit 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

AT3G07480.1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

At2g46540/F11C10.23

Excitatory amino acid transporter

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B

At4g16450

P1

unknown

Uncharacterized protein At2g27730, mitochondrial

Gamma carbonic anhydrase-like 2, mitochondrial

Gamma carbonic anhydrase 2, mitochondrial

Gamma carbonic anhydrase 1, mitochondrial

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