SMTL ID : 5xtd.1

Cryo-EM structure of human respiratory complex I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.179, P.197, S.352, C.353, G.354, Q.355, C.356, C.359, T.397, I.398, C.399, L.401 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.353 SF4.3: 12 residues within 4Å: Chain B: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, A.130, I.131 1 PLIP interactions: 1 interactions with chain B, Metal complexes: B:C.80 SF4.4: 13 residues within 4Å: Chain B: H.65, C.87, P.88, I.92, I.111, C.116, I.117, Y.118, C.119, G.120, F.121, C.122, E.133 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:E.133 Metal complexes: B:C.87, B:C.116, B:C.119 SF4.6: 12 residues within 4Å: Chain C: A.30, C.31, C.32, G.67, T.68, G.94, S.95, C.96, C.126, P.127 Chain P: R.105, H.190 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.31, C:C.32, C:C.96, C:C.126 SF4.9: 11 residues within 4Å: Chain L: H.95, D.98, C.99, C.102, Q.104, G.105, C.108, L.110, Q.111, V.199, G.200 3 PLIP interactions: 3 interactions with chain L, Metal complexes: L:H.95, L:C.99, L:C.108 SF4.10: 10 residues within 4Å: Chain L: C.147, I.148, C.150, C.153, V.177, C.197, P.198, V.199, A.201, L.202 5 PLIP interactions: 5 interactions with chain L, Metal complexes: L:C.147, L:C.150, L:C.150, L:C.153, L:C.197

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 13 residues within 4Å: Chain A: G.61, R.62, G.63, N.90, D.92, E.93, Y.178, G.181, E.182, E.183, A.217, N.218, A.400 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.90, A:D.92, A:N.218 Hydrogen bonds: A:R.62, A:G.63, A:N.90, A:E.182, A:E.183, A:E.183, A:A.217, A:N.218, A:T.221, A:A.400

9 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.5: 20 residues within 4Å: Chain B: T.24, L.25, W.27, L.30, F.31 Chain P: R.233, R.236, N.237 Chain S: V.17 Chain U: L.37 Chain f: W.179, P.180, M.183, M.184, F.186, I.273, Y.277, F.280, L.288, N.292 18 PLIP interactions: 9 interactions with chain f, 3 interactions with chain P, 4 interactions with chain B, 1 interactions with chain U, 1 interactions with chain S Hydrophobic interactions: f:W.179, f:P.180, f:F.186, f:F.186, f:I.273, f:Y.277, f:F.280, f:L.288, B:W.27, B:L.30, B:F.31, U:L.37, S:V.17 Hydrogen bonds: f:N.292, P:N.237, B:T.24 Salt bridges: P:R.233, P:R.233 PLX.13: 13 residues within 4Å: Chain 7: A.103, W.106, L.107, D.112 Chain S: L.8, A.11, E.15, L.18, S.21, F.22, G.25 Chain f: P.295, M.302 9 PLIP interactions: 1 interactions with chain f, 4 interactions with chain 7, 4 interactions with chain S Hydrophobic interactions: f:P.295, 7:A.103, 7:W.106, 7:L.107, S:L.18, S:F.22, S:F.22 Salt bridges: 7:D.112 Hydrogen bonds: S:E.15 PLX.16: 12 residues within 4Å: Chain 9: L.553, W.557, L.558, L.561 Chain T: N.106, Y.107, G.108, A.111 Chain c: P.81, S.86, A.90, F.94 12 PLIP interactions: 4 interactions with chain 9, 5 interactions with chain c, 3 interactions with chain T Hydrophobic interactions: 9:L.553, 9:W.557, 9:L.558, 9:L.561, c:P.81, c:F.94, c:F.94, c:F.94, T:A.111 Hydrogen bonds: c:S.86, T:Y.107, T:G.108 PLX.18: 11 residues within 4Å: Chain 1: R.43 Chain 2: Y.55 Chain Y: A.32, T.36, N.39, Q.44, H.64 Chain Z: Y.84, Y.88, E.92 Ligands: PLX.30 9 PLIP interactions: 3 interactions with chain Z, 1 interactions with chain 1, 5 interactions with chain Y Hydrophobic interactions: Z:Y.84, Y:A.32, Y:T.36, Y:N.39 Hydrogen bonds: Z:Y.84, Y:Q.44 Salt bridges: Z:E.92, 1:R.43, Y:H.64 PLX.19: 12 residues within 4Å: Chain 4: N.6, P.9, L.10, F.12, R.77 Chain 5: P.1, F.2 Chain 6: T.132, W.133, Y.143, I.209, I.346 6 PLIP interactions: 2 interactions with chain 4, 4 interactions with chain 6 Hydrogen bonds: 4:N.6, 6:I.346 Salt bridges: 4:R.77 Hydrophobic interactions: 6:W.133, 6:I.209, 6:I.346 PLX.20: 9 residues within 4Å: Chain 3: H.35, N.36 Chain 4: K.24, L.25, T.26, F.35, I.64, F.68 Ligands: CDL.22 5 PLIP interactions: 4 interactions with chain 4, 1 interactions with chain 3 Hydrophobic interactions: 4:F.35, 4:I.64, 4:F.68 Hydrogen bonds: 4:L.25 Salt bridges: 3:H.35 PLX.21: 11 residues within 4Å: Chain 3: K.16, T.20 Chain 4: R.48, R.50, R.59, L.62, Y.63, A.66, F.67 Chain 6: P.324, F.325 10 PLIP interactions: 2 interactions with chain 6, 7 interactions with chain 4, 1 interactions with chain 3 Hydrophobic interactions: 6:P.324, 4:R.59, 4:Y.63, 4:Y.63, 4:A.66, 4:F.67 Hydrogen bonds: 6:F.325, 4:R.50 Salt bridges: 4:R.59, 3:K.16 PLX.29: 13 residues within 4Å: Chain T: Y.116 Chain c: Y.101 Chain e: N.188, S.189, W.190, N.193, L.194, L.197, H.256, M.257, Y.259, P.260, L.264 9 PLIP interactions: 7 interactions with chain e, 1 interactions with chain c, 1 interactions with chain T Hydrophobic interactions: e:W.190, e:W.190, e:N.193, e:L.197, e:P.260, e:L.264, T:Y.116 Hydrogen bonds: e:N.193, c:Y.101 PLX.30: 14 residues within 4Å: Chain 2: S.50, V.53, A.54, Y.55 Chain 9: I.16, W.66 Ligands: PLX.18 Chain e: L.68, W.71, P.443, L.446, L.447, L.449, N.450 11 PLIP interactions: 8 interactions with chain e, 2 interactions with chain 9, 1 interactions with chain 2 Hydrophobic interactions: e:L.68, e:W.71, e:P.443, e:L.446, e:L.447, e:L.447, e:N.450, 9:I.16, 9:W.66, 2:V.53 Hydrogen bonds: e:N.450

2 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Non-covalent)

8Q1.7: 14 residues within 4Å: Chain D: M.10, V.17, L.20, W.24, V.48, M.51, F.52, N.55, A.56, V.58, V.64, L.67, V.68 Chain F: S.41 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.20, D:W.24, D:V.48, D:F.52, D:V.58, D:V.64 Hydrogen bonds: D:K.14 8Q1.28: 20 residues within 4Å: Chain V: D.40, S.41, L.42 Chain d: H.5, Q.6, V.9, A.16, H.19, L.20, M.37, R.40, F.41, H.44, K.45, E.47, A.53, L.56, A.60, F.64, R.67 11 PLIP interactions: 8 interactions with chain d, 3 interactions with chain V Hydrophobic interactions: d:V.9, d:H.19, d:L.20, d:F.41, d:K.45, d:A.60, d:F.64, d:R.67 Hydrogen bonds: V:S.41, V:S.41, V:L.42

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

NDP.8: 22 residues within 4Å: Chain I: G.21, T.23, G.24, F.25, L.26, C.47, A.71, L.90, I.91, G.92, R.93, F.100, F.106, V.128, S.129, H.130, Y.141, K.145, P.164, D.166, I.167, R.173 16 PLIP interactions: 16 interactions with chain I Hydrophobic interactions: I:H.130, I:P.164, I:I.167 Hydrogen bonds: I:T.23, I:F.25, I:L.26, I:L.90, I:G.92, I:R.93, I:K.145, I:I.167, I:I.167 Salt bridges: I:R.93, I:R.93, I:R.173, I:R.173

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

FES.11: 10 residues within 4Å: Chain L: R.33, C.35, Y.36, A.43, N.45, C.46, R.47, M.48, C.49, C.63 1 PLIP interactions: 1 interactions with chain L, Metal complexes: L:C.46 FES.12: 9 residues within 4Å: Chain N: C.100, T.102, P.104, C.105, C.141, L.142, G.143, A.144, C.145 2 PLIP interactions: 2 interactions with chain N, Metal complexes: N:C.141, N:C.145

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 14 residues within 4Å: Chain 6: P.110, H.112, F.113, L.160, A.164 Chain 9: I.576, T.577 Chain T: T.34, Y.38, R.39, L.42, N.43, Y.58, T.61 9 PLIP interactions: 2 interactions with chain 6, 6 interactions with chain T, 1 interactions with chain 9 Hydrophobic interactions: 6:P.110, 6:L.160, T:Y.38, T:Y.58, 9:T.577 Hydrogen bonds: T:N.43, T:N.43, T:Y.58 Salt bridges: T:R.39 CDL.22: 17 residues within 4Å: Chain 4: Y.38, C.39, L.46, I.52, A.53 Chain 6: T.238, W.239, T.241, P.242, L.243 Ligands: PLX.20 Chain e: W.16, L.17, S.90, K.93, L.94 Chain i: H.294 11 PLIP interactions: 4 interactions with chain 4, 4 interactions with chain e, 3 interactions with chain 6 Hydrophobic interactions: 4:Y.38, 4:L.46, 4:L.46, 4:A.53, e:W.16, e:L.94, 6:P.242, 6:L.243 Hydrogen bonds: e:S.90, 6:T.238 Salt bridges: e:K.93 CDL.25: 18 residues within 4Å: Chain 9: T.22, L.23, P.26, K.28, Q.116, K.119, Y.120, I.123, T.127, M.150, L.153 Chain Y: L.17, L.20, R.21 Chain e: L.354, F.357, L.360, F.438 12 PLIP interactions: 2 interactions with chain e, 2 interactions with chain Y, 8 interactions with chain 9 Hydrophobic interactions: e:F.357, e:F.438, Y:L.20, 9:L.23, 9:L.23, 9:T.127 Salt bridges: Y:R.21, 9:K.28, 9:K.119, 9:K.119, 9:K.119 Hydrogen bonds: 9:Y.120 CDL.26: 7 residues within 4Å: Chain 0: D.115 Chain 9: L.184, S.209, T.211, L.214, L.272 Chain e: N.390 3 PLIP interactions: 3 interactions with chain 9 Hydrophobic interactions: 9:T.211 Hydrogen bonds: 9:S.209, 9:S.209 CDL.27: 14 residues within 4Å: Chain 4: T.26, P.28, L.31, Y.32 Chain 6: L.337, P.338 Chain b: Y.24, K.28, R.32 Chain e: T.55, F.121 Chain g: F.166, W.167, K.169 12 PLIP interactions: 5 interactions with chain 4, 2 interactions with chain e, 4 interactions with chain b, 1 interactions with chain 6 Hydrophobic interactions: 4:L.31, 4:Y.32, e:F.121, e:F.121, 6:L.337 Hydrogen bonds: 4:T.26 Salt bridges: 4:K.24, 4:K.24, b:K.28, b:K.28, b:R.32, b:R.32

4 x PEE: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)(Covalent)

PEE.15: 10 residues within 4Å: Chain 6: M.163, L.276, I.277, T.280, T.284 Chain T: W.132 Ligands: PEE.23 Chain e: P.159, Y.166, A.191 7 PLIP interactions: 3 interactions with chain 6, 4 interactions with chain e Hydrophobic interactions: 6:L.276, 6:I.277, 6:T.284, e:P.159, e:Y.166 Hydrogen bonds: e:Y.166, e:Y.166 PEE.17: 17 residues within 4Å: Chain 7: F.3, A.4, L.7 Chain Q: H.40 Chain U: F.134, M.135, Y.137, T.138 Chain a: V.37, L.44, F.56, R.136 Chain f: T.76, L.77, L.98, N.99, F.104 11 PLIP interactions: 3 interactions with chain a, 4 interactions with chain 7, 3 interactions with chain f, 1 interactions with chain U Hydrophobic interactions: a:L.44, a:F.56, 7:F.3, 7:F.3, 7:A.4, 7:L.7, f:L.77, f:F.104 Salt bridges: a:R.136 Hydrogen bonds: f:N.99, U:F.134 PEE.23: 12 residues within 4Å: Chain 6: I.285, L.288, Y.291, R.295 Chain 9: P.563, S.567, Q.570, I.571 Chain P: Q.13, Y.20 Ligands: PEE.15 Chain e: V.155 12 PLIP interactions: 3 interactions with chain P, 2 interactions with chain e, 7 interactions with chain 6 Hydrogen bonds: P:Q.13, P:Q.13, P:Y.20, 6:Y.291 Hydrophobic interactions: e:V.155, e:V.155, 6:I.285, 6:L.288, 6:Y.291, 6:Y.291 Salt bridges: 6:R.295, 6:R.295 PEE.24: 15 residues within 4Å: Chain 0: N.82, R.83 Chain 9: T.166, Q.170, L.173, Y.174, M.533, H.534, I.537, P.538, G.541, T.544 Chain e: S.274, L.277, L.405 11 PLIP interactions: 9 interactions with chain 9, 2 interactions with chain e Hydrophobic interactions: 9:L.173, 9:Y.174, 9:I.537, 9:P.538, e:L.277, e:L.405 Hydrogen bonds: 9:T.166, 9:Q.170, 9:Q.170 Salt bridges: 9:H.534, 9:H.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R. et al., Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell (2017)

Release Date

2017-08-30

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: E
Acyl carrier protein, mitochondrial: FV
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: G
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: H
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: I
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: J
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: K
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: M
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: N
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: P
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: T
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: Z
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: 1
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 3
NADH dehydrogenase [ubiquinone] 1 subunit C2: 4
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 5
NADH-ubiquinone oxidoreductase chain 2: 6
NADH-ubiquinone oxidoreductase chain 3: 7
NADH-ubiquinone oxidoreductase chain 4L: 8
NADH-ubiquinone oxidoreductase chain 5: 9
NADH-ubiquinone oxidoreductase chain 6: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: d
NADH-ubiquinone oxidoreductase chain 4: e
NADH-ubiquinone oxidoreductase chain 1: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: g
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

V
X

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
S

R
T

S
U

T
V

U
W

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
l

a
m

b
n

c
o

d
p

e
r

f
s

g
u

h
v

i
w

Membrane

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

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

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 7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

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

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

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

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH-ubiquinone oxidoreductase chain 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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

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