SMTL ID : 7zdp.1

Complex I from Ovis aries at pH9, Open state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)

ZMP.1: 17 residues within 4Å: Chain K: D.112, S.113, L.114 Chain W: H.11, Q.12, V.15, L.18, A.22, L.43, R.46, F.47, H.50, K.51, L.63, A.66, E.69, F.70 8 PLIP interactions: 7 interactions with chain W, 1 interactions with chain K Hydrophobic interactions: W:V.15, W:V.15, W:A.22, W:L.43, W:K.51, W:A.66, W:F.70, K:L.114 ZMP.17: 16 residues within 4Å: Chain f: M.11, K.15, V.18, R.19, W.25, V.49, M.52, F.53, K.54, N.56, A.57, V.65, F.92 Chain i: D.112, S.113, L.114 11 PLIP interactions: 9 interactions with chain f, 2 interactions with chain i Hydrophobic interactions: f:K.15, f:W.25, f:W.25, f:V.49, f:F.53, f:V.65, f:F.92, i:L.114 Hydrogen bonds: f:K.15, i:S.113 Salt bridges: f:K.54

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 13 residues within 4Å: Chain N: I.31, K.35, S.36, E.53, L.79, F.82, Y.83, Q.97, L.100, R.104, R.126, F.134, Y.198 5 PLIP interactions: 5 interactions with chain N Hydrogen bonds: N:Q.97, N:Y.198 Salt bridges: N:K.35, N:R.126 pi-Stacking: N:F.134

1 x MYR: MYRISTIC ACID(Covalent)

MYR.3: 8 residues within 4Å: Chain F: L.413, Y.485, L.486, T.489 Chain V: G.1, A.2, L.4 Chain Y: T.121 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.413, F:L.486, F:T.489

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

SF4.4: 13 residues within 4Å: Chain 3: I.177, P.195, S.350, C.351, G.352, Q.353, C.354, C.357, T.395, I.396, C.397, L.399, G.400 4 PLIP interactions: 4 interactions with chain 3, Metal complexes: 3:C.351, 3:C.354, 3:C.357, 3:C.397 SF4.8: 10 residues within 4Å: Chain 5: H.96, D.99, C.100, C.103, G.106, C.109, L.111, Q.112, V.200, G.201 4 PLIP interactions: 4 interactions with chain 5, Metal complexes: 5:H.96, 5:C.100, 5:C.103, 5:C.109 SF4.9: 13 residues within 4Å: Chain 5: M.145, C.148, I.149, C.151, T.152, R.153, C.154, I.197, C.198, P.199, V.200, A.202, L.203 4 PLIP interactions: 4 interactions with chain 5, Metal complexes: 5:C.148, 5:C.151, 5:C.154, 5:C.198 SF4.12: 12 residues within 4Å: Chain 7: A.30, C.31, C.32, G.67, G.94, S.95, C.96, G.125, C.126, P.127 Chain A: R.138, H.223 4 PLIP interactions: 4 interactions with chain 7, Metal complexes: 7:C.31, 7:C.32, 7:C.96, 7:C.126 SF4.13: 12 residues within 4Å: Chain 8: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 5 PLIP interactions: 5 interactions with chain 8, Salt bridges: 8:E.133 Metal complexes: 8:C.87, 8:C.116, 8:C.119, 8:C.122 SF4.14: 13 residues within 4Å: Chain 8: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, V.128, A.130, I.131 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.77, 8:C.80, 8:C.83, 8:C.126

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 20 residues within 4Å: Chain 3: G.59, R.60, G.61, A.63, K.70, N.88, D.90, E.91, G.92, Y.176, I.177, G.179, E.180, E.181, A.215, N.216, T.219, A.398, L.399 Ligands: NAI.6 14 PLIP interactions: 14 interactions with chain 3 Hydrophobic interactions: 3:Y.176, 3:I.177, 3:A.398, 3:L.399 Hydrogen bonds: 3:R.60, 3:G.61, 3:N.88, 3:E.91, 3:G.92, 3:E.180, 3:E.181, 3:E.181, 3:N.216 Salt bridges: 3:K.70

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.6: 16 residues within 4Å: Chain 3: G.61, G.62, A.63, F.65, K.70, F.73, E.93, Y.176, E.180, E.181, K.198, F.201, S.295, T.323, A.398 Ligands: FMN.5 10 PLIP interactions: 10 interactions with chain 3 Hydrophobic interactions: 3:E.93, 3:T.323 Hydrogen bonds: 3:G.61, 3:K.70, 3:E.181, 3:S.295 Salt bridges: 3:K.198, 3:K.198 pi-Stacking: 3:F.65, 3:F.201

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

FES.7: 9 residues within 4Å: Chain 4: C.99, T.101, P.103, C.104, C.140, L.141, G.142, A.143, C.144 4 PLIP interactions: 4 interactions with chain 4, Metal complexes: 4:C.99, 4:C.104, 4:C.140, 4:C.144 FES.10: 9 residues within 4Å: Chain 5: R.34, C.36, Y.37, G.45, N.46, C.47, R.48, C.50, C.64 4 PLIP interactions: 4 interactions with chain 5, Metal complexes: 5:C.36, 5:C.47, 5:C.50, 5:C.64

1 x K: POTASSIUM ION(Non-covalent)

K.11: 5 residues within 4Å: Chain 5: Q.105, I.195, C.198, V.200, L.203 2 PLIP interactions: 2 interactions with chain 5 Metal complexes: 5:I.195, 5:C.198

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 4 residues within 4Å: Chain a: C.59, H.68, C.84, C.87 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.59, a:H.68, a:C.84, a:C.87

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

NDP.16: 25 residues within 4Å: Chain 7: R.156 Chain c: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, V.130, G.131, R.132, E.133, F.139, V.144, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, I.206, R.212 20 PLIP interactions: 19 interactions with chain c, 1 interactions with chain 7 Hydrophobic interactions: c:P.203, c:I.206 Hydrogen bonds: c:G.60, c:T.62, c:F.64, c:L.65, c:L.129, c:E.133, c:E.133, c:Y.180, c:Y.180, c:K.184 Salt bridges: c:R.85, c:R.132, c:R.132, c:R.212, c:R.212, 7:R.156 pi-Cation interactions: c:R.85, c:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kravchuk, V. et al., A universal coupling mechanism of respiratory complex I. Nature (2022)

Release Date

2022-09-21

Peptides

Complex I-49kD: A
NADH-ubiquinone oxidoreductase chain 3: B
NADH-ubiquinone oxidoreductase chain 1: C
NADH-ubiquinone oxidoreductase chain 6: D
NADH-ubiquinone oxidoreductase chain 4L: E
NADH-ubiquinone oxidoreductase chain 5: F
NADH-ubiquinone oxidoreductase chain 4: G
NADH-ubiquinone oxidoreductase chain 2: H
Complex I-B14.7: I
Complex I-SGDH: J
Acyl carrier protein: Ki
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: L
Complex I-PDSW: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: O
Complex I-B9: P
Complex I-B12: Q
NADH dehydrogenase [ubiquinone] 1 subunit C2: R
NADH:ubiquinone oxidoreductase subunit B4: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: T
Mitochondrial complex I, B17 subunit: U
Complex I-B18: V
Complex I-B22: W
Complex I-AGGG: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: Y
Complex I-ESSS: Z
Complex I-KFYI: 0
Complex I-MNLL: 1
Complex I-MWFE: 2
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: 3
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: 4
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: 5
Complex I-30kD: 6
Complex I-20kD: 7
Complex I-23kD: 8
Complex I-9kD: 9
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: a
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: b
NADH:ubiquinone oxidoreductase subunit A9: c
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: d
Complex I subunit B13: e
Complex I-B14: f
Mitochondrial complex I, B14.5a subunit: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

B
A

C
H

D
J

E
K

F
L

G
M

H
N

I
V

J
W

K
X

i
j

L
Y

M
Z

N
k

O
l

P
m

Q
n

R
o

S
p

T
q

U
r

V
s

W
t

X
u

Y
v

Z
w

0
x

1
y

2
z

3
1

4
2

5
3

6
5

7
6

8
9

9
a

a
b

b
c

c
d

d
e

e
f

f
g

g
h

h
i

Membrane

We predict this structure to be a membrane protein.
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Complex I-49kD

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

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

Complex I-B14.7

Complex I-SGDH

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

Complex I-PDSW

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

Complex I-B9

Complex I-B12

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Mitochondrial complex I, B17 subunit

Complex I-B18

Complex I-B22

Complex I-AGGG

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

Complex I-ESSS

Complex I-KFYI

Complex I-MNLL

Complex I-MWFE

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

Complex I-30kD

Complex I-20kD

Complex I-23kD

Complex I-9kD

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Complex I subunit B13

Complex I-B14

Mitochondrial complex I, B14.5a subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

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