SMTL ID : 7a23.1

Plant mitochondrial respiratory complex I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.228, P.246, S.401, C.402, G.403, Q.404, C.405, C.408, R.409, T.446, I.447, C.448, L.450 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.402, A:C.405, A:C.408, A:C.448 SF4.9: 13 residues within 4Å: Chain N: M.306, I.310 Chain O: H.166, D.169, C.170, C.173, Q.175, G.176, C.179, L.181, Q.182, V.270, G.271 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:H.166, O:C.170, O:C.173, O:C.179 SF4.10: 13 residues within 4Å: Chain O: M.215, C.218, I.219, Q.220, C.221, T.222, R.223, C.224, I.248, C.268, P.269, V.270, L.273 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.218, O:C.221, O:C.224, O:C.268 SF4.15: 11 residues within 4Å: Chain N: R.69, H.154 Chain W: A.92, C.93, C.94, G.129, G.156, S.157, C.158, C.188, P.189 5 PLIP interactions: 5 interactions with chain W, Metal complexes: W:C.93, W:C.94, W:C.158, W:C.188, W:C.188 SF4.16: 13 residues within 4Å: Chain X: H.111, C.133, P.134, I.138, I.157, C.162, I.163, Y.164, C.165, G.166, F.167, C.168, E.179 5 PLIP interactions: 5 interactions with chain X, Salt bridges: X:E.179 Metal complexes: X:C.133, X:C.162, X:C.165, X:C.168 SF4.17: 13 residues within 4Å: Chain X: C.123, I.124, A.125, C.126, K.127, L.128, C.129, I.140, Y.155, C.172, P.173, A.176, I.177 4 PLIP interactions: 4 interactions with chain X, Metal complexes: X:C.123, X:C.126, X:C.129, X:C.172

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 23 residues within 4Å: Chain A: G.110, R.111, G.112, G.113, A.114, K.121, N.139, D.141, E.142, E.144, D.150, Y.227, G.230, E.231, E.232, V.265, T.266, N.267, T.270, T.374, A.449, L.450, A.453 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.227, A:E.231, A:E.231, A:A.449, A:A.453 Hydrogen bonds: A:R.111, A:G.112, A:G.113, A:A.114, A:G.115, A:K.121, A:N.139, A:E.144, A:D.150, A:V.265, A:N.267 Salt bridges: A:K.121

2 x T7X: Phosphatidylinositol(Non-covalent)

T7X.3: 20 residues within 4Å: Chain B: W.56, F.99, L.102, A.105, S.109, F.350, L.354, R.463, N.464, L.467, L.468, M.471, F.475 Chain L: T.16, Q.17, R.24, P.32, H.35, M.39 Ligands: CDL.4 15 PLIP interactions: 5 interactions with chain L, 10 interactions with chain B Hydrophobic interactions: L:T.16, L:P.32, L:M.39, B:F.99, B:L.102, B:A.105, B:F.350, B:L.468, B:F.475 Hydrogen bonds: L:R.24, L:R.24, B:R.463, B:R.463, B:N.464 Salt bridges: B:R.463 T7X.20: 17 residues within 4Å: Chain 3: R.82, A.85, V.86, G.89, V.90, I.93 Chain 5: F.13, R.16 Chain 6: L.22, L.25, L.29, R.36 Chain Z: T.46, Y.49, L.50, I.53 Ligands: CDL.4 9 PLIP interactions: 3 interactions with chain 3, 3 interactions with chain 6, 1 interactions with chain Z, 2 interactions with chain 5 Hydrophobic interactions: 3:V.86, 3:I.93, 6:L.22, 5:F.13, 5:R.16 Salt bridges: 3:R.82 Hydrogen bonds: 6:R.36, 6:R.36, Z:Y.49

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 17 residues within 4Å: Chain 3: I.93 Chain 6: T.18, A.21, L.22, L.25 Chain B: W.56, R.463 Chain L: H.31, P.32, E.34, H.35 Chain Z: I.43, T.46, V.47, L.50 Ligands: T7X.3, T7X.20 13 PLIP interactions: 1 interactions with chain B, 5 interactions with chain Z, 2 interactions with chain 3, 1 interactions with chain L, 4 interactions with chain 6 Salt bridges: B:R.463, Z:K.54, L:H.31 Hydrophobic interactions: Z:I.43, Z:T.46, Z:V.47, Z:L.50, 3:I.93, 3:I.93, 6:T.18, 6:A.21, 6:L.22, 6:L.25 CDL.5: 20 residues within 4Å: Chain 3: N.81 Chain B: N.27, I.31, I.34, V.38, F.39, S.42, K.44, Y.45 Chain C: F.101, T.104, L.108, K.112 Chain J: F.10, C.21 Chain Z: G.59, P.60, T.64, L.67 Ligands: CDL.6 16 PLIP interactions: 2 interactions with chain C, 1 interactions with chain J, 2 interactions with chain Z, 9 interactions with chain B, 2 interactions with chain 3 Hydrophobic interactions: C:F.101, C:T.104, J:F.10, Z:P.60, Z:L.67, B:N.27, B:I.31, B:I.31, B:V.38, B:V.38, B:F.39 Salt bridges: B:K.44, B:K.44, B:K.44 Hydrogen bonds: 3:N.81, 3:N.81 CDL.6: 15 residues within 4Å: Chain B: I.23, I.26, N.27 Chain C: F.91, W.94, M.97, A.98, F.101 Chain D: F.149, V.150, L.153 Chain Z: A.21, F.22, T.23 Ligands: CDL.5 12 PLIP interactions: 5 interactions with chain C, 1 interactions with chain Z, 2 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: C:F.91, C:W.94, C:A.98, C:F.101, C:F.101, D:F.149, D:V.150, B:I.23, B:I.23, B:I.23, B:I.26 Hydrogen bonds: Z:F.22

1 x U10: UBIQUINONE-10(Non-covalent)

U10.7: 17 residues within 4Å: Chain E: A.21, V.24, R.28, P.51, L.52, D.54, G.55, L.56, L.58, E.207, L.212, F.225, F.229, L.230, R.284 Chain W: W.85, I.114 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain W Hydrophobic interactions: E:A.21, E:V.24, E:L.52, E:L.56, E:F.225, E:F.225, E:F.229, E:F.229, E:L.230, W:W.85 Hydrogen bonds: E:R.284

1 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.8: 32 residues within 4Å: Chain E: F.184, P.185, V.188, M.189, F.191, I.192, F.203, V.283, F.287, Y.290, L.298, V.302, F.303, L.306, W.310 Chain H: M.49, F.50, V.53, S.54, F.57 Chain J: Q.13, P.15, V.16, I.23 Chain N: R.197, Q.201 Chain X: T.70, L.71, F.72, L.73, M.76, V.77 29 PLIP interactions: 16 interactions with chain E, 6 interactions with chain X, 3 interactions with chain H, 3 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: E:F.184, E:V.188, E:V.188, E:F.191, E:I.192, E:I.192, E:I.192, E:F.203, E:V.283, E:F.287, E:Y.290, E:L.298, E:W.310, E:W.310, X:L.71, X:F.72, X:F.72, X:L.73, X:L.73, X:V.77, H:F.50, H:V.53, H:F.57, J:I.23 Hydrogen bonds: E:Y.290, E:Y.290, N:Q.201 Salt bridges: N:R.197, N:R.197

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

FES.11: 9 residues within 4Å: Chain O: R.104, F.105, C.106, Y.107, C.117, R.118, C.120, A.132, C.134 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.106, O:C.117, O:C.117, O:C.134 FES.13: 9 residues within 4Å: Chain R: C.130, P.134, C.135, C.171, M.172, G.173, C.174, C.175, M.180 5 PLIP interactions: 5 interactions with chain R, Metal complexes: R:C.130, R:C.135, R:C.171, R:C.174, R:C.175

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

NDP.12: 22 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, F.154, A.159, V.183, C.185, K.200, P.219, A.220, T.221, M.222, R.228, I.229 14 PLIP interactions: 14 interactions with chain P Hydrogen bonds: P:G.75, P:T.77, P:T.77, P:T.77, P:F.79, P:L.80, P:L.144, P:G.146, P:M.222 Salt bridges: P:R.100, P:R.147, P:R.147, P:R.228 pi-Cation interactions: P:R.100

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain T: C.72, H.82, C.97, C.100 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:C.72, T:H.82, T:C.97 ZN.18: 3 residues within 4Å: Chain 5: H.107 Chain 6: H.130 Ligands: BCT.19 2 PLIP interactions: 1 interactions with chain 6, 1 interactions with chain 5 Metal complexes: 6:H.130, 5:H.107

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.19: 6 residues within 4Å: Chain 5: H.107, V.108, H.135 Chain 6: Q.101, Y.207 Ligands: ZN.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soufari, H. et al., Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Nat Commun (2020)

Release Date

2020-10-28

Peptides

51kDa: A
Nad2m: B
Nad3m: C
Nad6m: D
Nad1m: E
Nad4Lm: F
PGIV: G
B16.6: H
MWFE: I
B9: J
B14.5a: K
B14.5b: L
15kDa: M
Nad7m: N
75kDa: O
39kDa: P
Nad9m: Q
24kDa: R
18kDa: S
13kDa: T
B13: U
B17.2: V
PSST: W
TYKY: X
B14: Y
20.9kDa: Z
B8: 0
ACPM1: 1
Unk1: 2
P2: 3
CAL1: 4
CA1: 56
Nad4m: 7
PDSW: 8
ESSS: 9
B22: a
Nad5m: b
B18: c
AGGG: d
ACPM2: e
B15: f
Unk2: g
P1: h
B12-1: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

C
J

D
N

E
H

F
K

G
Y

H
Z

I
V

J
W

K
S

L
i

M
j

N
G

O
C

P
T

Q
F

R
B

S
O

T
P

U
R

V
U

W
E

X
D

Y
X

Z
c

0
Q

1
k

2
r

3
n

4
o

5
q

6
p

7
M

8
f

9
g

a
d

b
a

c
b

d
h

e
e

f
l

g
s

h
m

i
t

Membrane

We predict this structure to be a membrane protein.
Show / Hide

51kDa

Nad2m

Nad3m

Nad6m

Nad1m

Nad4Lm

PGIV

B16.6

MWFE

B9

B14.5a

B14.5b

15kDa

Nad7m

75kDa

39kDa

Nad9m

24kDa

18kDa

13kDa

B13

B17.2

PSST

TYKY

B14

20.9kDa

B8

ACPM1

Unk1

P2

CAL1

CA1

Nad4m

PDSW

ESSS

B22

Nad5m

B18

AGGG

ACPM2

B15

Unk2

P1

B12-1

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