SMTL ID : 7zdm.1

Complex I from Ovis aries at pH5.5, Closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.379, A:C.382, A:C.385, A:C.425 SF4.5: 12 residues within 4Å: Chain C: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.124, C:C.128, C:C.131, C:C.137 SF4.6: 10 residues within 4Å: Chain C: C.176, I.177, C.179, T.180, R.181, C.182, C.226, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.176, C:C.179, C:C.182, C:C.226 SF4.10: 11 residues within 4Å: Chain D: R.138, H.223 Chain F: A.97, C.98, C.99, G.134, G.161, S.162, C.163, C.193, P.194 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.98, F:C.99, F:C.163, F:C.193 SF4.14: 11 residues within 4Å: Chain G: H.106, C.128, P.129, I.133, C.157, I.158, Y.159, C.160, G.161, F.162, C.163 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.174 Metal complexes: G:C.128, G:C.157, G:C.163 SF4.15: 12 residues within 4Å: Chain G: C.118, I.119, A.120, C.121, K.122, L.123, C.124, I.135, Y.150, C.167, V.169, I.172 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.118, G:C.121, G:C.124, G:C.167

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 21 residues within 4Å: Chain A: G.87, R.88, G.89, A.91, K.98, N.116, D.118, E.119, G.120, Y.204, I.205, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 Ligands: NAI.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.204, A:I.205, A:E.208, A:A.426, A:L.427 Hydrogen bonds: A:G.89, A:E.119, A:G.120, A:E.209, A:N.244 Salt bridges: A:K.98

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

NAI.3: 16 residues within 4Å: Chain A: G.89, G.90, A.91, F.93, K.98, F.101, E.121, Y.204, E.209, K.226, F.229, P.230, S.323, T.351, A.426 Ligands: FMN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.121, A:T.351 Hydrogen bonds: A:G.89, A:K.98, A:E.209, A:S.323 Salt bridges: A:K.226, A:K.226 pi-Stacking: A:F.229

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

FES.4: 9 residues within 4Å: Chain B: C.132, T.134, P.136, C.137, C.173, L.174, G.175, A.176, C.177 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.137, B:C.173, B:C.177 FES.7: 9 residues within 4Å: Chain C: R.62, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.64, C:C.75, C:C.78, C:C.92

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain C: Q.133, I.223, C.226, V.228, L.231 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:I.223, C:L.231

10 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.9: 16 residues within 4Å: Chain D: W.43, Q.46, M.52, Y.53 Chain V: L.562, P.563, S.567, Q.570, M.571 Chain W: N.144, F.151, Y.152 Chain X: I.284, L.288, Y.291 Ligands: PC1.26 11 PLIP interactions: 3 interactions with chain W, 4 interactions with chain V, 4 interactions with chain X Hydrophobic interactions: W:F.151, W:Y.152, V:L.562, V:P.563, V:Q.570, V:Q.570, X:L.288, X:L.288, X:L.288, X:Y.291 Hydrogen bonds: W:N.144 3PE.12: 13 residues within 4Å: Chain F: R.69, V.73, K.76, L.80, W.83, R.86, K.212 Chain P: R.29, W.75 Chain S: L.46, I.49, I.53 Ligands: PC1.11 13 PLIP interactions: 8 interactions with chain F, 4 interactions with chain S, 1 interactions with chain P Hydrophobic interactions: F:V.73, F:K.76, F:L.80, F:W.83, S:L.46, S:I.49, S:I.49, S:I.53 Salt bridges: F:R.86, F:R.86, F:K.212, F:K.212 Hydrogen bonds: P:R.29 3PE.19: 16 residues within 4Å: Chain 5: F.8, V.12, E.16, L.19, V.20, S.22, F.23, A.26, G.27 Chain R: F.96, A.99, A.103, W.106, T.107 Chain S: P.295, M.302 9 PLIP interactions: 4 interactions with chain R, 4 interactions with chain 5, 1 interactions with chain S Hydrophobic interactions: R:F.96, R:A.99, R:A.103, R:T.107, 5:F.8, 5:V.12, 5:V.20, 5:F.23, S:P.295 3PE.20: 22 residues within 4Å: Chain 9: F.140, I.141, W.142, Y.143, T.144 Chain R: L.3, M.4, L.7 Chain S: L.73, M.98, N.99, L.100, F.104, M.108 Chain T: I.34, V.35, V.39, G.42, L.45, N.46, S.50 Chain i: A.39 12 PLIP interactions: 3 interactions with chain S, 2 interactions with chain R, 6 interactions with chain T, 1 interactions with chain 9 Hydrophobic interactions: S:L.73, R:L.3, R:L.7, T:I.34, T:V.35, T:V.39, T:L.45, T:L.45 Hydrogen bonds: S:N.99, S:L.100, T:S.50, 9:F.140 3PE.21: 14 residues within 4Å: Chain T: V.18, S.21, K.23, V.88, T.92, T.95, G.96 Chain U: V.14, T.17, M.21, Y.22, R.23 Chain V: K.585, L.596 8 PLIP interactions: 4 interactions with chain T, 2 interactions with chain V, 2 interactions with chain U Hydrophobic interactions: T:V.18, T:V.88, T:T.95, V:L.596, U:M.21 Salt bridges: T:K.23, V:K.585 Hydrogen bonds: U:R.23 3PE.22: 18 residues within 4Å: Chain V: T.166, Q.170, L.173, Y.174, L.218, T.221, L.229, Y.529, M.533, H.534, T.537, P.538, N.541 Chain W: L.398, L.405 Chain e: N.115, R.116, V.117 12 PLIP interactions: 1 interactions with chain W, 11 interactions with chain V Hydrophobic interactions: W:L.398, V:L.173, V:Y.174, V:L.218, V:T.221, V:T.537, V:P.538, V:P.538, V:N.541 Hydrogen bonds: V:Q.170 Salt bridges: V:H.534, V:H.534 3PE.25: 11 residues within 4Å: Chain W: N.188, W.190, M.201, L.212, M.257, P.260, F.261 Chain Y: D.86, P.87, L.88, M.127 6 PLIP interactions: 4 interactions with chain W, 2 interactions with chain Y Hydrophobic interactions: W:L.212, W:P.260, W:F.261, W:F.261, Y:P.87, Y:L.88 3PE.27: 11 residues within 4Å: Chain 8: P.83, N.84, S.88, G.91, G.95, I.96 Chain V: W.557, L.558 Chain Y: Y.108, G.109, A.112 6 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain 8, 4 interactions with chain V Hydrogen bonds: Y:Y.108 Hydrophobic interactions: 8:I.96, V:W.557, V:W.557, V:W.557, V:L.558 3PE.28: 8 residues within 4Å: Chain Y: K.3, L.6, W.10, L.124, V.125, Q.129, V.135 Ligands: PC1.26 6 PLIP interactions: 6 interactions with chain Y Hydrophobic interactions: Y:L.6, Y:L.124, Y:V.125, Y:V.135 Hydrogen bonds: Y:Q.129 Salt bridges: Y:K.3 3PE.31: 9 residues within 4Å: Chain 4: P.2 Chain 7: Q.8, P.12, L.13, F.15, R.80 Chain X: Y.143, I.206, I.345 9 PLIP interactions: 2 interactions with chain 4, 5 interactions with chain 7, 2 interactions with chain X Hydrogen bonds: 4:P.2, 4:P.2, 7:Q.8, 7:L.13, 7:R.80 Hydrophobic interactions: 7:F.15, X:I.206, X:I.345 Salt bridges: 7:R.80

5 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.11: 14 residues within 4Å: Chain F: L.77, I.81, R.216, L.217, W.220, R.223 Chain K: D.90, F.310 Chain R: L.24, Q.26 Chain S: A.52, F.56, I.57 Ligands: 3PE.12 10 PLIP interactions: 2 interactions with chain K, 4 interactions with chain F, 3 interactions with chain S, 1 interactions with chain R Hydrophobic interactions: K:F.310, F:L.77, F:I.81, F:W.220, S:A.52, S:F.56, S:I.57, R:L.24 Salt bridges: K:D.90, F:R.223 PC1.13: 24 residues within 4Å: Chain 5: W.13, E.16, L.28 Chain 9: F.36 Chain D: R.266 Chain G: T.65, L.66, W.68, L.71 Chain S: I.175, W.179, P.180, M.183, F.186, I.187, P.197, F.198, I.273, Y.277, F.280, L.288, N.292, F.293, L.296 19 PLIP interactions: 13 interactions with chain S, 2 interactions with chain 5, 2 interactions with chain 9, 1 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: S:I.175, S:W.179, S:P.180, S:M.183, S:F.186, S:F.186, S:P.197, S:F.198, S:I.273, S:F.280, S:F.293, S:L.296, 5:W.13, 5:L.28, 9:F.36, 9:F.36, G:W.68 Hydrogen bonds: S:N.292 Salt bridges: D:R.266 PC1.23: 15 residues within 4Å: Chain V: W.66, H.67, W.68, S.77, L.78, N.136, F.138, I.142 Chain W: P.371, K.452 Ligands: PC1.24 Chain a: I.81, Y.85, H.89, K.93 13 PLIP interactions: 5 interactions with chain a, 7 interactions with chain V, 1 interactions with chain W Hydrophobic interactions: a:I.81, a:I.81, a:Y.85, V:W.66, V:W.66, V:W.68, V:L.78, V:F.138, V:I.142, W:P.371 Salt bridges: a:K.93, a:K.93 Hydrogen bonds: V:H.67 PC1.24: 22 residues within 4Å: Chain V: T.16, I.19, W.66, L.123 Chain W: P.64, I.67, L.68, W.71, P.443, L.446, L.447, L.449, N.450, I.453, I.454 Ligands: PC1.23 Chain f: V.98, L.99, S.103, V.106, A.107, Y.108 13 PLIP interactions: 1 interactions with chain f, 10 interactions with chain W, 2 interactions with chain V Hydrophobic interactions: f:L.99, W:P.64, W:I.67, W:L.68, W:W.71, W:W.71, W:P.443, W:L.447, W:L.447, W:I.453, W:I.454, V:I.19, V:L.123 PC1.26: 19 residues within 4Å: Chain V: I.566 Chain W: A.155, G.156, P.159, Y.166, S.191, F.194, L.197, A.198, M.201, V.205 Chain X: D.274, I.276, I.277, T.280 Chain Y: L.124, W.133 Ligands: 3PE.9, 3PE.28 17 PLIP interactions: 5 interactions with chain X, 8 interactions with chain W, 1 interactions with chain V, 3 interactions with chain Y Hydrophobic interactions: X:I.276, X:I.277, X:I.277, X:T.280, W:A.155, W:P.159, W:F.194, W:F.194, W:L.197, W:A.198, W:M.201, W:V.205, V:I.566, Y:L.124, Y:W.133 Hydrogen bonds: X:D.274 Salt bridges: Y:K.134

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 5 residues within 4Å: Chain I: C.87, G.89, H.96, C.112, C.115 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.87, I:H.96, I:C.112, I:C.115

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

NDP.17: 24 residues within 4Å: Chain F: R.223 Chain K: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, V.130, G.131, R.132, F.139, V.144, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, I.206, R.212 22 PLIP interactions: 21 interactions with chain K, 1 interactions with chain F Hydrophobic interactions: K:P.203, K:I.206 Hydrogen bonds: K:G.60, K:T.62, K:T.62, K:T.62, K:F.64, K:L.65, K:R.85, K:R.85, K:C.86, K:L.129, K:G.131, K:Y.180, K:Y.180, K:K.184 Salt bridges: K:R.85, K:R.132, K:R.212, K:R.212, F:R.223 pi-Cation interactions: K:R.85

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

ZMP.18: 13 residues within 4Å: Chain N: K.41, V.44, V.75, M.78, F.79, N.82, V.85, V.91, L.94, F.118 Chain Q: D.112, S.113, L.114 9 PLIP interactions: 7 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: N:K.41, N:F.79, N:V.91, N:F.118, N:F.118, Q:L.114 Hydrogen bonds: N:K.41, N:N.82, Q:S.113 ZMP.29: 12 residues within 4Å: Chain 0: D.112, S.113 Chain c: H.12, Q.13, V.16, A.23, R.47, F.48, H.51, K.52, A.67, F.71 8 PLIP interactions: 8 interactions with chain c Hydrophobic interactions: c:V.16, c:A.23, c:F.48, c:F.48, c:K.52, c:F.71 Hydrogen bonds: c:Q.13, c:Q.13

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.30: 13 residues within 4Å: Chain 3: I.66, K.70, S.71, E.88, Y.118, Q.132, L.135, R.139, R.161, D.166, F.169, M.173, Y.233 10 PLIP interactions: 10 interactions with chain 3 Hydrogen bonds: 3:E.88, 3:Y.118, 3:Q.132, 3:Q.132, 3:R.139, 3:R.161, 3:K.221 Salt bridges: 3:K.70, 3:R.161 pi-Stacking: 3:F.169

1 x MYR: MYRISTIC ACID(Covalent)

MYR.32: 10 residues within 4Å: Chain V: N.400, L.413, Y.485, L.486 Chain b: G.2, A.3, H.4, L.5 Chain e: T.152, Q.154 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain b Hydrophobic interactions: V:L.413, V:Y.485, V:L.486, b:L.5

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

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
Mitochondrial complex I, 24 kDa subunit: B
NADH:ubiquinone oxidoreductase core subunit S1: C
Complex I-49kD: D
NADH:ubiquinone oxidoreductase core subunit S3: E
Complex I-20kD: F
Complex I-23kD: G
Complex I-9kD: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: I
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: J
NADH:ubiquinone oxidoreductase subunit A9: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: L
Mitochondrial complex I, B13 subunit: M
NADH:ubiquinone oxidoreductase subunit A6: N
Mitochondrial complex I, B14.5a subunit: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: P
Acyl carrier protein: Q0
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 1: S
NADH-ubiquinone oxidoreductase chain 6: T
NADH-ubiquinone oxidoreductase chain 4L: U
NADH-ubiquinone oxidoreductase chain 5: V
NADH-ubiquinone oxidoreductase chain 4: W
NADH-ubiquinone oxidoreductase chain 2: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 1
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: 2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH:ubiquinone oxidoreductase subunit A3: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: 6
NADH dehydrogenase [ubiquinone] 1 subunit C2: 7
NADH:ubiquinone oxidoreductase subunit B4: 8
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: 9
Mitochondrial complex I, B17 subunit: a
NADH:ubiquinone oxidoreductase subunit B7: b
NADH:ubiquinone oxidoreductase subunit B9: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: e
Mitochondrial complex I, ESSS subunit: f
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: g
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: h
Complex I-MWFE: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
a

I
b

J
c

K
d

L
e

M
f

N
g

O
h

P
i

Q
j

0
X

R
A

S
H

T
J

U
K

V
L

W
M

X
N

Y
V

Z
W

1
Y

2
Z

3
k

4
l

5
m

6
n

7
o

8
p

9
q

a
r

b
s

c
t

d
u

e
v

f
w

g
x

h
y

i
z

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

Mitochondrial complex I, 24 kDa subunit

NADH:ubiquinone oxidoreductase core subunit S1

Complex I-49kD

NADH:ubiquinone oxidoreductase core subunit S3

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

Mitochondrial complex I, B13 subunit

NADH:ubiquinone oxidoreductase subunit A6

Mitochondrial complex I, B14.5a subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

Acyl carrier protein

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH:ubiquinone oxidoreductase subunit A3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Mitochondrial complex I, B17 subunit

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

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

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

Mitochondrial complex I, ESSS subunit

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

Complex I-MWFE

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