SMTL ID : 7ar8.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain B: A.92, C.93, C.94, G.129, T.130, G.156, S.157, C.158, G.187, C.188, P.189 Chain D: R.69, H.154 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.93, B:C.94, B:C.158, B:C.188 SF4.4: 13 residues within 4Å: Chain F: 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 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:S.401, F:C.402, F:C.405, F:C.408, F:C.448 SF4.6: 11 residues within 4Å: Chain D: M.306 Chain G: H.166, D.169, C.170, C.173, Q.175, G.176, C.179, Q.182, V.270, G.271 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.169 Metal complexes: G:H.166, G:C.170, G:C.173, G:C.179 SF4.7: 10 residues within 4Å: Chain G: C.218, I.219, C.221, T.222, R.223, C.224, I.248, C.268, V.270, L.273 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.218, G:C.221, G:C.224, G:C.268 SF4.10: 13 residues within 4Å: Chain I: H.111, C.133, P.134, A.135, I.138, C.162, I.163, Y.164, C.165, G.166, F.167, C.168, E.179 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.179 Metal complexes: I:C.133, I:C.162, I:C.165, I:C.168 SF4.11: 11 residues within 4Å: Chain I: C.123, I.124, A.125, C.126, K.127, C.129, I.140, Y.155, C.172, V.174, A.176 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.123, I:C.126, I:C.129, I:C.172

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

FES.2: 8 residues within 4Å: Chain E: C.130, G.131, P.134, C.135, M.169, C.171, C.175, M.180 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.135, E:C.171 FES.5: 10 residues within 4Å: Chain G: R.104, F.105, C.106, Y.107, G.115, N.116, C.117, R.118, C.120, C.134 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.106, G:N.116, G:C.117, G:C.120, G:C.134

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 19 residues within 4Å: Chain F: G.110, R.111, G.112, A.114, K.121, N.139, D.141, S.143, Y.227, I.228, G.230, E.231, E.232, V.265, T.266, N.267, T.270, A.449, L.450 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:I.228, F:E.231, F:E.231, F:A.449, F:L.450 Hydrogen bonds: F:R.111, F:G.112, F:A.114, F:N.139, F:D.141, F:S.143, F:S.143, F:V.265, F:N.267 Salt bridges: F:K.121

1 x UQ9: Ubiquinone-9(Covalent)

UQ9.8: 16 residues within 4Å: Chain B: W.85, I.114, R.116 Chain H: L.14, L.17, L.18, A.21, V.24, R.28, P.51, D.54, L.58, F.225, A.226, F.229, L.230 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain B Hydrophobic interactions: H:L.14, H:L.17, H:L.18, H:L.18, H:D.54, H:L.58, H:F.225, H:F.229, H:L.230, B:W.85 pi-Stacking: H:F.229 Hydrogen bonds: B:R.116, B:R.116

3 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Covalent)

PTY.9: 27 residues within 4Å: Chain 0: P.15, V.16, I.23 Chain D: R.197 Chain H: P.185, L.187, V.188, M.189, F.191, I.192, P.202, F.275, F.276, L.279, F.287, Y.290, L.298, V.302, F.303, L.306, W.310 Chain I: T.70, L.71, F.72, L.73, M.76 Chain Y: V.53 19 PLIP interactions: 12 interactions with chain H, 1 interactions with chain 0, 1 interactions with chain Y, 2 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: H:P.185, H:L.187, H:V.188, H:F.191, H:F.191, H:I.192, H:P.202, H:F.275, H:F.276, H:F.287, H:F.303, H:W.310, 0:I.23, Y:V.53, I:L.71, I:F.72, I:L.73 Salt bridges: D:R.197, D:R.197 PTY.13: 11 residues within 4Å: Chain 5: I.74, L.77, G.78, L.81, N.82 Chain M: I.461, V.465, W.469, Y.473, K.475, V.476 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain 5 Hydrophobic interactions: M:I.461, M:I.461, M:V.465, M:V.465, M:Y.473, M:Y.473, 5:I.74 Hydrogen bonds: M:Y.473 Salt bridges: M:K.475 PTY.15: 22 residues within 4Å: Chain 2: L.12, T.16, Q.17, E.34, V.37, G.42 Chain N: W.56, L.102, G.106, S.109, L.354, M.357, D.462, R.463, N.464, L.467, M.471, F.474, F.475 Ligands: PGT.14, LMN.20, PSF.24 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: N:L.354, N:L.354, N:L.467, N:F.474, N:F.475, 2:V.37 Hydrogen bonds: N:R.463 Salt bridges: N:R.463, N:R.463

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(Non-covalent)

PC7.12: 25 residues within 4Å: Chain 1: R.16, S.21, M.22, T.23, G.24, P.26 Chain L: L.10, S.14, F.18, H.109, R.112, Y.116, I.119, L.145, L.149 Chain M: V.371, S.372, P.375, S.378, T.379, F.382, F.383, L.391, P.392, Y.433 18 PLIP interactions: 7 interactions with chain M, 1 interactions with chain 1, 10 interactions with chain L Hydrophobic interactions: M:V.371, M:T.379, M:F.382, M:F.382, M:F.383, M:L.391, L:L.10, L:F.18, L:Y.116, L:I.119, L:L.145, L:L.149 Hydrogen bonds: M:S.378, 1:G.24, L:Y.116 Salt bridges: L:H.109, L:R.112, L:R.112 PC7.22: 10 residues within 4Å: Chain 4: G.59, P.60, V.63, T.64, L.67 Chain N: I.34, F.39, Y.45 Chain h: K.80, N.81 9 PLIP interactions: 3 interactions with chain N, 1 interactions with chain h, 5 interactions with chain 4 Hydrophobic interactions: N:I.34, N:F.39, 4:P.60, 4:V.63, 4:V.63, 4:L.67 Hydrogen bonds: N:Y.45, h:N.81, 4:G.59

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

PGT.14: 7 residues within 4Å: Chain 4: L.50, K.54 Chain N: W.56 Ligands: PTY.15, PSF.24, T7X.25 Chain j: K.233 2 PLIP interactions: 1 interactions with chain j, 1 interactions with chain 4 Salt bridges: j:K.233 Hydrophobic interactions: 4:L.50

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

FE.16: 5 residues within 4Å: Chain O: H.83, C.91, C.95, L.133, C.135 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:H.83, O:C.91, O:C.95

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

NDP.17: 19 residues within 4Å: Chain P: G.75, T.77, G.78, F.79, L.80, R.100, P.125, L.144, I.145, G.146, R.147, E.148, F.154, I.163, V.183, C.185, K.200, M.222, R.228 14 PLIP interactions: 14 interactions with chain P Hydrogen bonds: P:T.77, P:T.77, P:F.79, P:L.80, P:R.100, P:L.144, P:M.222 Salt bridges: P:R.100, P:R.147, P:R.228, P:R.228 pi-Stacking: P:F.154 pi-Cation interactions: P:R.100, P:R.100

2 x ZN: ZINC ION(Non-covalent)

ZN.18: 5 residues within 4Å: Chain R: C.72, G.74, H.82, C.97, C.100 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.72, R:H.82, R:C.97, R:C.100 ZN.23: 4 residues within 4Å: Chain j: H.107, H.135 Chain k: H.130, Y.207 4 PLIP interactions: 2 interactions with chain j, 2 interactions with chain k Metal complexes: j:H.107, j:H.135, k:H.130, k:Y.207

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

8Q1.19: 16 residues within 4Å: Chain U: D.82, S.83 Chain W: R.23, F.29, Q.62, I.63, N.66, A.67, I.75, L.78, I.79, G.82, E.85, L.86, I.89, Y.103 11 PLIP interactions: 10 interactions with chain W, 1 interactions with chain U Hydrophobic interactions: W:F.29, W:F.29, W:A.67, W:I.75, W:L.86, W:I.89, W:Y.103 Hydrogen bonds: W:N.66, W:A.67, U:S.83 Salt bridges: W:R.23 8Q1.21: 15 residues within 4Å: Chain T: S.79, L.80 Chain b: R.13, K.17, R.19, V.20, L.23, L.48, K.51, F.52, Q.56, V.58, G.71, Y.75, W.78 14 PLIP interactions: 13 interactions with chain b, 1 interactions with chain T Hydrophobic interactions: b:K.17, b:L.23, b:L.48, b:K.51, b:V.58, b:Y.75, b:W.78, b:W.78 Hydrogen bonds: b:R.19, b:R.19, b:F.52, T:S.79 Salt bridges: b:K.17, b:R.21

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

LMN.20: 19 residues within 4Å: Chain 2: I.3, S.4, A.5, V.8, L.12, G.42, F.45, A.46, L.49, V.50, K.51, V.54, K.57 Chain M: R.73, E.78 Chain N: L.478, L.481, Y.482 Ligands: PTY.15 20 PLIP interactions: 4 interactions with chain M, 5 interactions with chain N, 11 interactions with chain 2 Hydrogen bonds: M:R.73, M:E.78, M:E.78, N:Y.482, 2:S.4, 2:K.51 Salt bridges: M:R.73, 2:K.51 Hydrophobic interactions: N:L.478, N:L.481, N:L.481, N:Y.482, 2:I.3, 2:A.5, 2:V.8, 2:L.12, 2:F.45, 2:A.46, 2:L.49, 2:V.50

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

PSF.24: 9 residues within 4Å: Chain 2: W.33, E.34 Chain N: R.463 Ligands: PGT.14, PTY.15, T7X.25 Chain k: L.22, R.24, R.28 6 PLIP interactions: 1 interactions with chain N, 5 interactions with chain k Salt bridges: N:R.463, k:R.24, k:R.28, k:R.28 Hydrophobic interactions: k:L.22 Hydrogen bonds: k:R.24

1 x T7X: Phosphatidylinositol(Non-covalent)

T7X.25: 13 residues within 4Å: Chain 4: T.46, Y.49, L.50, I.53 Ligands: PGT.14, PSF.24 Chain h: V.86, G.89, V.90 Chain j: W.14, T.18 Chain k: L.25, R.28 6 PLIP interactions: 1 interactions with chain h, 4 interactions with chain k, 1 interactions with chain j Hydrophobic interactions: h:V.90, k:L.25, k:L.25, j:W.14 Hydrogen bonds: k:R.28 Salt bridges: k: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

2021-12-15

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 subunit 7: 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 dehydrogenase subunit 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
AT3G07480.1: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: S
Acyl carrier protein 1, mitochondrial: T
Acyl carrier protein 2, mitochondrial: U
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Z
At2g46540/F11C10.23: 0
Transmembrane protein: 1
Excitatory amino acid transporter: 2
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B: 3
At4g16450: 4
ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein: 5
P1: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: 9
B15 -- 1 beta subcomplex subunit 4: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B: d
Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: e
Furry: f
unknown: g
Uncharacterized protein At2g27730, mitochondrial: h
Gamma carbonic anhydrase-like 2, mitochondrial: i
Gamma carbonic anhydrase 2, mitochondrial: j
Gamma carbonic anhydrase 1, mitochondrial: k

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
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Z

Z
a

0
b

1
c

2
d

3
e

4
f

5
g

6
i

7
j

8
k

9
l

a
m

b
n

c
o

d
p

e
q

f
r

g
u

h
v

i
x

j
y

k
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 subunit 7

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 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 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-B

At4g16450

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

P1

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

B15 -- 1 beta subcomplex subunit 4

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

Furry

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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