SMTL ID : 7ar7.1

Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain B: A.31, C.32, C.33, G.68, T.69, G.95, S.96, C.97, G.126, C.127, P.128 Chain D: R.60, H.145 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.32, B:C.33, B:C.97, B:C.127 SF4.4: 13 residues within 4Å: Chain F: I.178, P.196, S.351, C.352, G.353, Q.354, C.355, C.358, T.396, I.397, C.398, L.400, G.401 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:S.351, F:C.352, F:C.355, F:C.358, F:C.398 SF4.6: 11 residues within 4Å: Chain D: M.297 Chain G: H.110, D.113, C.114, C.117, Q.119, G.120, C.123, Q.126, V.214, G.215 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.113 Metal complexes: G:H.110, G:C.114, G:C.117, G:C.123 SF4.7: 10 residues within 4Å: Chain G: C.162, I.163, C.165, T.166, R.167, C.168, I.192, C.212, V.214, L.217 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.162, G:C.165, G:C.168, G:C.212 SF4.9: 13 residues within 4Å: Chain I: H.58, C.80, P.81, A.82, I.85, C.109, I.110, Y.111, C.112, G.113, F.114, C.115, E.126 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.126 Metal complexes: I:C.80, I:C.109, I:C.112, I:C.115 SF4.10: 11 residues within 4Å: Chain I: C.70, I.71, A.72, C.73, K.74, C.76, I.87, Y.102, C.119, V.121, A.123 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.70, I:C.73, I:C.76, I:C.119

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

FES.2: 10 residues within 4Å: Chain E: G.102, T.103, C.106, S.111, M.140, C.142, C.146, N.148, A.149, M.151 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.106, E:C.142, E:C.142, E:C.146 FES.5: 10 residues within 4Å: Chain G: R.48, F.49, C.50, Y.51, G.59, N.60, C.61, R.62, C.64, C.78 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.50, G:N.60, G:C.61, G:C.64, G:C.78

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain F: G.60, R.61, G.62, A.64, K.71, N.89, D.91, S.93, Y.177, I.178, G.180, E.181, E.182, V.215, T.216, N.217, T.220, A.399, L.400 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:I.178, F:E.181, F:A.399, F:L.400 Hydrogen bonds: F:R.61, F:G.62, F:N.89, F:D.91, F:S.93, F:E.182, F:V.215, F:N.217 Salt bridges: F:K.71

1 x UQ9: Ubiquinone-9(Covalent)

UQ9.8: 14 residues within 4Å: Chain B: W.24, R.55 Chain H: L.13, L.16, L.17, A.20, V.23, R.27, P.50, D.53, L.57, A.225, F.228, L.229 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: H:L.13, H:L.16, H:L.17, H:L.17, H:L.17, H:D.53, H:L.57, H:A.225, H:L.229 Hydrogen bonds: H:R.27, B:R.55 pi-Stacking: H:F.228, B:W.24

3 x PTY: PHOSPHATIDYLETHANOLAMINE(Covalent)

PTY.11: 21 residues within 4Å: Chain D: R.188, Q.192 Chain H: P.184, L.186, V.187, M.188, F.190, F.202, F.275, L.278, F.286, L.297, L.305, W.309 Chain I: T.17, L.18, F.19, L.20, M.23 Chain X: V.35, F.39 21 PLIP interactions: 11 interactions with chain H, 3 interactions with chain D, 5 interactions with chain I, 2 interactions with chain X Hydrophobic interactions: H:P.184, H:L.186, H:V.187, H:F.190, H:F.202, H:F.275, H:L.278, H:F.286, H:L.305, H:W.309, H:W.309, I:L.18, I:F.19, I:F.19, I:L.20, I:L.20, X:V.35, X:F.39 Hydrogen bonds: D:Q.192 Salt bridges: D:R.188, D:R.188 PTY.13: 12 residues within 4Å: Chain 4: I.43, L.46, G.47, L.50, N.51, D.55 Chain M: L.335, V.457, V.460, W.461, Y.465, V.468 10 PLIP interactions: 4 interactions with chain 4, 6 interactions with chain M Hydrophobic interactions: 4:I.43, 4:L.46, M:L.335, M:V.457, M:W.461, M:Y.465, M:Y.465 Hydrogen bonds: 4:N.51, 4:D.55, M:Y.465 PTY.15: 21 residues within 4Å: Chain 1: T.15, Q.16, E.33, G.37, F.44 Chain N: W.45, F.88, L.91, G.95, S.98, L.343, M.346, R.452, N.453, L.456, M.460, F.463, F.464 Ligands: LMN.14, PGT.22, PSF.23 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain 1 Hydrophobic interactions: N:W.45, N:F.88, N:L.343, N:N.453, N:L.456, N:F.463, N:F.464, 1:F.44 Salt bridges: N:R.452, N:R.452

2 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Covalent)

PC7.12: 27 residues within 4Å: Chain 0: R.4, V.7, S.9, T.11, G.12 Chain L: L.10, S.13, S.14, G.17, F.18, H.109, R.112, C.115, Y.116, I.119, F.122 Chain M: V.363, S.364, T.365, P.367, S.370, T.371, F.374, F.375, L.378, T.386, Y.425 13 PLIP interactions: 4 interactions with chain M, 9 interactions with chain L Hydrophobic interactions: M:V.363, M:F.375, M:T.386, L:L.10, L:F.18, L:F.18, L:Y.116, L:I.119, L:I.119, L:F.122 Hydrogen bonds: M:S.370 Salt bridges: L:H.109, L:R.112 PC7.19: 13 residues within 4Å: Chain 3: G.59, P.60, M.62, V.63, T.64, L.67, L.70 Chain N: I.20, I.23, F.28, Y.34 Chain g: N.8, Y.11 13 PLIP interactions: 5 interactions with chain 3, 6 interactions with chain N, 2 interactions with chain g Hydrophobic interactions: 3:V.63, 3:V.63, 3:L.67, 3:L.70, N:I.20, N:I.23, N:I.23, N:F.28, N:F.28, g:Y.11 Hydrogen bonds: 3:G.59, N:Y.34, g:N.8

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

LMN.14: 19 residues within 4Å: Chain 1: I.2, S.3, A.4, V.7, L.11, G.41, F.44, A.45, L.48, V.49, V.53, K.56 Chain M: L.64, R.65, E.70 Chain N: L.467, L.470, Y.471 Ligands: PTY.15 14 PLIP interactions: 4 interactions with chain N, 7 interactions with chain 1, 3 interactions with chain M Hydrophobic interactions: N:L.467, N:L.470, N:Y.471, 1:A.4, 1:V.7, 1:F.44, 1:A.45, 1:L.48, 1:V.49, M:L.64 Hydrogen bonds: N:Y.471, 1:S.3, M:R.65 Salt bridges: M:R.65

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

NDP.16: 18 residues within 4Å: Chain B: K.157 Chain O: G.24, T.26, G.27, F.28, L.29, R.49, P.74, L.93, I.94, G.95, R.96, F.103, C.134, K.149, T.170, M.171, R.177 16 PLIP interactions: 15 interactions with chain O, 1 interactions with chain B Hydrogen bonds: O:T.26, O:T.26, O:T.26, O:T.26, O:F.28, O:L.29, O:G.95, O:G.95, O:M.171 Salt bridges: O:R.49, O:R.96, O:R.96, O:R.177, O:R.177, B:K.157 pi-Cation interactions: O:R.49

2 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain Q: C.25, H.35, C.50, C.53 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.25, Q:H.35, Q:C.50, Q:C.53 ZN.21: 5 residues within 4Å: Chain i: R.85, H.106, H.134 Chain j: H.129, Y.206 2 PLIP interactions: 1 interactions with chain j, 1 interactions with chain i Metal complexes: j:Y.206, i:H.106

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

8Q1.18: 18 residues within 4Å: Chain T: D.39, S.40, L.41 Chain V: R.23, V.26, F.29, I.40, I.59, Q.62, I.63, N.66, A.67, I.75, L.78, I.79, L.86, I.89, Y.103 13 PLIP interactions: 3 interactions with chain T, 10 interactions with chain V Hydrophobic interactions: T:L.41, V:V.26, V:F.29, V:I.40, V:I.59, V:Q.62, V:I.75, V:L.86, V:Y.103 Hydrogen bonds: T:D.39, T:S.40, V:N.66 Salt bridges: V:R.23 8Q1.20: 15 residues within 4Å: Chain L: T.548 Chain S: S.42, L.43 Chain a: Q.10, K.11, V.14, L.17, K.45, F.46, Q.50, V.52, G.65, E.68, K.71, W.72 10 PLIP interactions: 9 interactions with chain a, 1 interactions with chain S Hydrophobic interactions: a:F.46, a:K.71, a:W.72, a:W.72, a:W.72 Hydrogen bonds: a:Q.10, a:F.46, a:Q.50, S:S.42 Salt bridges: a:K.11

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

PGT.22: 7 residues within 4Å: Chain 3: L.50, K.54 Chain N: W.45 Ligands: PTY.15, PSF.23, T7X.24 Chain i: K.232 6 PLIP interactions: 1 interactions with chain i, 1 interactions with chain j, 1 interactions with chain N, 3 interactions with chain 3 Salt bridges: i:K.232, 3:K.54 Hydrogen bonds: j:R.35 Hydrophobic interactions: N:W.45, 3:L.50, 3:L.50

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

PSF.23: 10 residues within 4Å: Chain 1: W.32, E.33 Chain N: R.452 Ligands: PTY.15, PGT.22, T7X.24 Chain h: Y.198 Chain j: L.21, R.23, R.27 5 PLIP interactions: 4 interactions with chain j, 1 interactions with chain N Hydrophobic interactions: j:L.21 Hydrogen bonds: j:R.23 Salt bridges: j:R.23, j:R.27, N:R.452

1 x T7X: Phosphatidylinositol(Non-covalent)

T7X.24: 14 residues within 4Å: Chain 3: T.46, Y.49, L.50, I.53 Ligands: PGT.22, PSF.23 Chain g: R.9, A.12, V.13, V.17 Chain i: W.13, T.17 Chain j: L.24, R.27 8 PLIP interactions: 2 interactions with chain i, 4 interactions with chain j, 1 interactions with chain 3, 1 interactions with chain g Hydrophobic interactions: i:W.13, i:W.13, j:L.24, j:L.24, 3:T.46, g:V.17 Hydrogen bonds: j:R.27 Salt bridges: j:R.27

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

2022-03-02

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial: I
NADH-ubiquinone oxidoreductase chain 6: J
NADH-ubiquinone oxidoreductase chain 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: R
Acyl carrier protein 1, mitochondrial: S
Acyl carrier protein 2, mitochondrial: T
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Y
At2g46540/F11C10.23: Z
Transmembrane protein: 0
Excitatory amino acid transporter: 1
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A: 2
At4g16450: 3
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein: 4
At1g67350: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: 8
AT2G31490 protein: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B: c
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: d
B14.5a: e
unknown: f
Uncharacterized protein At2g27730, mitochondrial: g
Gamma carbonic anhydrase-like 2, mitochondrial: h
Gamma carbonic anhydrase 2, mitochondrial: i
Gamma carbonic anhydrase 1, mitochondrial: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
P

P
Q

Q
R

R
S

S
T

T
U

U
V

V
W

W
X

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
i

6
j

7
k

8
l

9
m

a
n

b
o

c
p

d
q

e
r

f
u

g
v

h
x

i
y

j
z

Membrane

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

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

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

NADH-ubiquinone oxidoreductase chain 1

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

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

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 1, 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 8-B

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

At2g46540/F11C10.23

Transmembrane protein

Excitatory amino acid transporter

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

At4g16450

ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein

At1g67350

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

AT2G31490 protein

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B

Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

B14.5a

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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