SMTL ID : 7arb.1

Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition)

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 SF4.5: 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 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.402, F:C.405, F:C.408, F:C.448 SF4.7: 11 residues within 4Å: Chain D: M.306 Chain G: H.166, D.169, C.170, C.173, Q.175, G.176, C.179, L.181, 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 SF4.8: 11 residues within 4Å: Chain G: 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 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: 12 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, I.177 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.123, I:C.126, I:C.129, I:C.172

3 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 23 residues within 4Å: Chain 0: P.15, V.16 Chain D: R.197, Q.201 Chain H: F.184, P.185, V.188, F.191, F.203, F.275, 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 17 PLIP interactions: 2 interactions with chain I, 3 interactions with chain D, 10 interactions with chain H, 1 interactions with chain Y, 1 interactions with chain 0 Hydrophobic interactions: I:F.72, I:L.73, H:F.184, H:P.185, H:V.188, H:F.191, H:F.203, H:F.275, H:F.287, H:F.303, H:W.310, H:W.310, Y:V.53 Hydrogen bonds: D:Q.201, 0:E.14 Salt bridges: D:R.197, D:R.197 PTY.12: 12 residues within 4Å: Chain 5: I.74, L.77, G.78, L.81, N.82 Chain M: I.95, I.461, V.465, V.468, W.469, Y.473, V.476 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain 5 Hydrophobic interactions: M:I.95, M:I.461, M:V.468, M:W.469, M:Y.473, 5:L.77 Hydrogen bonds: M:Y.473, 5:N.82 Salt bridges: M:K.475 PTY.14: 20 residues within 4Å: Chain 2: T.16, Q.17, E.34, V.37, G.38, G.42 Chain N: W.56, L.102, A.105, G.106, S.109, M.357, R.463, N.464, L.467, M.471, F.475 Ligands: LMN.13, PGT.20, PSF.25 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain 2 Hydrophobic interactions: N:L.102, N:A.105, N:L.467, N:M.471, N:F.475, 2:V.37 Hydrogen bonds: N:N.464, N:N.464 Salt bridges: N:R.463

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

FES.3: 8 residues within 4Å: Chain E: G.131, C.135, S.140, M.169, C.171, C.175, A.178, M.180 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.171, E:C.175 FES.6: 8 residues within 4Å: Chain G: R.104, C.106, Y.107, G.115, C.117, R.118, C.120, C.134 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.106, G:C.117, G:C.120, G:C.134

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 19 residues within 4Å: Chain F: G.110, R.111, G.112, A.114, K.121, N.139, D.141, E.142, S.143, Y.227, G.230, E.231, E.232, V.265, T.266, N.267, T.270, A.449, L.450 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Y.227, F:E.231, F:E.231, F:A.449, F:L.450 Hydrogen bonds: F:G.112, F:N.139, F:S.143, F:G.230, F:E.232, F:E.232, F:N.267, F:N.267 Salt bridges: F:K.121

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

UQ9.9: 16 residues within 4Å: Chain B: W.85, I.114, R.116 Chain H: L.14, P.15, L.17, L.18, A.21, V.24, P.51, D.54, L.58, F.225, A.226, F.229, L.230 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:P.15, H:L.18, H:A.21, H:P.51, H:L.58, H:F.229, H:F.229, H:L.230, H:L.230 pi-Stacking: H:F.229

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

LMN.13: 18 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, V.54, K.57 Chain M: R.73, E.78 Chain N: L.478, L.481, Y.482 Ligands: PTY.14 13 PLIP interactions: 4 interactions with chain N, 7 interactions with chain 2, 2 interactions with chain M Hydrophobic interactions: N:L.478, N:L.481, N:Y.482, 2:A.5, 2:V.8, 2:L.12, 2:F.45, 2:L.49, 2:V.50 Hydrogen bonds: N:Y.482, 2:K.57, M:R.73 Salt bridges: M:R.73

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

FE.15: 4 residues within 4Å: Chain O: H.83, C.91, C.95, C.135 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:H.83, O:C.91, O:C.95, O:C.135

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

NDP.16: 23 residues within 4Å: Chain B: K.218 Chain P: G.75, T.77, G.78, F.79, L.80, R.100, P.125, L.144, I.145, G.146, R.147, F.154, I.163, V.183, S.184, C.185, K.200, P.219, A.220, T.221, M.222, R.228 19 PLIP interactions: 18 interactions with chain P, 1 interactions with chain B Hydrogen bonds: P:G.75, P:T.77, P:T.77, P:T.77, P:F.79, P:L.80, P:R.100, P:L.144, P:G.146, P:R.147, P:K.200, P:M.222 Salt bridges: P:R.100, P:R.147, P:R.147, P:R.228, P:R.228, B:K.218 pi-Cation interactions: P:R.100

2 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain R: C.72, 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.24: 5 residues within 4Å: Chain j: H.107, H.135 Chain k: Q.101, 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)

8Q1.18: 20 residues within 4Å: Chain U: D.82, S.83, L.84 Chain W: R.23, V.26, F.27, F.29, I.40, I.59, Q.62, I.63, N.66, A.67, I.69, I.75, L.78, G.82, L.86, I.89, Y.103 14 PLIP interactions: 11 interactions with chain W, 3 interactions with chain U Hydrophobic interactions: W:V.26, W:F.29, W:I.40, W:I.59, W:A.67, W:I.75, W:L.86, W:L.86, W:Y.103, U:L.84 Hydrogen bonds: W:N.66, U:D.82, U:S.83 Salt bridges: W:R.23 8Q1.22: 19 residues within 4Å: Chain T: S.79, L.80 Chain b: K.17, V.20, R.21, L.23, A.27, D.30, L.48, K.51, F.52, N.55, Q.56, V.58, I.64, G.71, E.74, Y.75, W.78 14 PLIP interactions: 11 interactions with chain b, 3 interactions with chain T Hydrophobic interactions: b:K.17, b:V.20, b:L.23, b:A.27, b:L.48, b:K.51, b:F.52, b:Y.75, b:W.78, T:L.80 Hydrogen bonds: b:N.55, T:S.79, T:S.79 Salt bridges: b:K.17

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)

PC7.19: 27 residues within 4Å: Chain 1: S.21, M.22, T.23, G.25, P.26 Chain L: L.10, S.14, G.17, F.18, H.109, R.112, C.115, Y.116, I.119, F.122, F.123, L.145, L.149 Chain M: V.371, S.372, P.375, S.378, T.379, F.382, F.383, L.391, Y.433 20 PLIP interactions: 6 interactions with chain M, 11 interactions with chain L, 3 interactions with chain 1 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:F.18, L:Y.116, L:I.119, L:F.122, L:F.123, L:L.145, L:L.149 Salt bridges: L:H.109, L:R.112 Hydrogen bonds: 1:S.21, 1:S.21, 1:G.25 PC7.23: 14 residues within 4Å: Chain 4: V.45, G.59, P.60, M.62, V.63, T.64, G.66, L.67, L.70 Chain N: I.31, I.34, F.39 Chain h: N.81, Y.84 11 PLIP interactions: 2 interactions with chain h, 5 interactions with chain N, 4 interactions with chain 4 Hydrophobic interactions: h:Y.84, N:I.31, N:I.34, N:I.34, N:F.39, N:F.39, 4:V.45, 4:V.63, 4:L.70 Hydrogen bonds: 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.20: 8 residues within 4Å: Chain 4: L.50, S.51, K.54 Chain N: W.56 Ligands: PTY.14, T7X.21, PSF.25 Chain j: K.233 2 PLIP interactions: 1 interactions with chain 4, 1 interactions with chain N Salt bridges: 4:K.54 Hydrophobic interactions: N:W.56

1 x T7X: Phosphatidylinositol(Non-covalent)

T7X.21: 15 residues within 4Å: Chain 4: T.46, Y.49, L.50, I.53 Ligands: PGT.20, PSF.25 Chain h: R.82, A.85, G.89, V.90 Chain j: I.15, T.18 Chain k: L.22, L.25, R.28 6 PLIP interactions: 3 interactions with chain k, 1 interactions with chain h, 1 interactions with chain j, 1 interactions with chain 4 Hydrophobic interactions: k:L.22, k:L.22, k:L.25, h:V.90, j:I.15, 4:T.46

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

PSF.25: 10 residues within 4Å: Chain 2: W.33, E.34 Chain N: R.463 Ligands: PTY.14, PGT.20, T7X.21 Chain i: Y.238 Chain k: L.22, R.24, R.28 8 PLIP interactions: 1 interactions with chain N, 6 interactions with chain k, 1 interactions with chain i Salt bridges: N:R.463, k:R.24, k:R.28 Hydrophobic interactions: k:L.22 Hydrogen bonds: k:R.24, k:R.28, k:R.28, i:Y.238

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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