SMTL ID : 6g72.1

Mouse mitochondrial complex I in the deactive state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain B: A.98, C.99, C.100, G.135, T.136, S.163, C.164, C.194, P.195 Chain D: R.118, R.138, H.223 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.99, B:C.100, B:C.164, B:C.194, B:C.194 SF4.4: 12 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:E.377 Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.5: 10 residues within 4Å: Chain G: H.124, D.127, C.128, C.131, Q.133, C.137, Q.140, R.175, V.228, G.229 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.6: 8 residues within 4Å: Chain G: M.173, C.176, I.177, C.179, T.180, C.182, C.226, L.231 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.8: 11 residues within 4Å: Chain I: H.101, C.123, I.128, C.152, I.153, Y.154, C.155, G.156, F.157, C.158, E.169 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:C.123, I:C.152, I:C.155, I:C.158 SF4.9: 12 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, L.118, C.119, I.130, Y.145, C.162, P.163, A.166, I.167 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.113, I:C.116, I:C.119, I:C.162

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

FES.2: 10 residues within 4Å: Chain E: C.134, T.136, P.138, C.139, C.175, L.176, G.177, A.178, C.179 Chain F: P.122 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.134, E:C.139, E:C.175, E:C.179 FES.7: 8 residues within 4Å: Chain G: R.62, F.63, C.64, G.73, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 20 residues within 4Å: Chain F: G.87, R.88, G.89, G.90, F.93, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Y.204, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:G.89, F:F.93, F:K.98, F:N.116, F:D.118, F:N.244, F:N.244, F:N.244, F:T.247 Salt bridges: F:K.98

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.10: 15 residues within 4Å: Chain O: N.65, I.66, C.67, S.68, G.69, K.70, N.71, Y.118, Q.132, L.135, R.139, E.160, F.169, K.221, E.226 9 PLIP interactions: 9 interactions with chain O Hydrogen bonds: O:I.66, O:S.68, O:Y.118, O:Q.132, O:Q.132, O:R.139, O:E.160, O:R.161 Salt bridges: O:K.221

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

NDP.11: 21 residues within 4Å: Chain B: R.224 Chain P: G.60, T.62, G.63, F.64, L.65, R.85, W.108, A.110, L.129, I.130, G.131, R.132, F.139, V.144, F.145, V.167, H.169, K.184, I.206, R.212 17 PLIP interactions: 1 interactions with chain B, 16 interactions with chain P Salt bridges: B:R.224, P:R.85, P:R.132, P:R.212, P:R.212 Hydrophobic interactions: P:I.206 Hydrogen bonds: P:G.60, P:T.62, P:G.63, P:F.64, P:L.65, P:R.85, P:L.129, P:G.131, P:K.184, P:R.212 pi-Cation interactions: P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain R: C.79, H.88, C.104, C.107 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.79, R:H.88, R:C.104, R:C.107

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Covalent)

EHZ.13: 17 residues within 4Å: Chain T: S.112 Chain W: K.32, L.55, I.57, G.62, V.66, M.69, F.70, N.73, A.74, V.76, L.85, G.89, E.92, V.106, F.109, F.110 12 PLIP interactions: 12 interactions with chain W Hydrophobic interactions: W:L.55, W:I.57, W:V.66, W:M.69, W:N.73, W:V.106, W:F.109, W:F.109, W:F.110, W:F.110 Hydrogen bonds: W:N.73 Salt bridges: W:K.32 EHZ.14: 16 residues within 4Å: Chain U: D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, H.26, M.44, R.47, F.48, H.51, K.52, A.67, F.71, N.74 12 PLIP interactions: 10 interactions with chain d, 2 interactions with chain U Hydrophobic interactions: d:K.52, d:A.67, d:F.71, d:F.71, d:F.71, d:N.74 Hydrogen bonds: d:Q.13, d:H.51, d:K.52, U:S.112, U:L.113 Salt bridges: d:K.52

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.15: 2 residues within 4Å: Chain g: M.1, E.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agip, A.A. et al., Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-06-06

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, 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 10, mitochondrial: 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, mitochondrial: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: X
MCG5603: Y
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: 1
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C2: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 8
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: i

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
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

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, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, 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 10, mitochondrial

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, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MCG5603

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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