SMTL ID : 5xtc.1

Cryo-EM structure of human respiratory complex I transmembrane arm

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-mer

Ligands

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

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 14 residues within 4Å: Chain D: T.34, Y.38, R.39, L.42, N.43, Y.58, T.61 Chain Q: P.110, H.112, F.113, L.160, A.164 Chain T: I.576, T.577 9 PLIP interactions: 6 interactions with chain D, 2 interactions with chain Q, 1 interactions with chain T Hydrophobic interactions: D:Y.38, D:Y.58, Q:P.110, Q:L.160, T:T.577 Hydrogen bonds: D:N.43, D:N.43, D:Y.58 Salt bridges: D:R.39 CDL.10: 17 residues within 4Å: Chain 2: H.294 Chain O: Y.38, C.39, L.46, I.52, A.53 Chain Q: T.238, W.239, T.241, P.242, L.243 Chain Y: W.16, L.17, S.90, K.93, L.94 Ligands: PLX.8 11 PLIP interactions: 4 interactions with chain O, 4 interactions with chain Y, 3 interactions with chain Q Hydrophobic interactions: O:Y.38, O:L.46, O:L.46, O:A.53, Y:W.16, Y:L.94, Q:P.242, Q:L.243 Hydrogen bonds: Y:S.90, Q:T.238 Salt bridges: Y:K.93 CDL.13: 18 residues within 4Å: Chain I: L.17, L.20, R.21 Chain T: 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.354, F.357, L.360, F.438 12 PLIP interactions: 8 interactions with chain T, 2 interactions with chain I, 2 interactions with chain Y Hydrophobic interactions: T:L.23, T:L.23, T:T.127, I:L.20, Y:F.357, Y:F.438 Hydrogen bonds: T:Y.120 Salt bridges: T:K.28, T:K.119, T:K.119, T:K.119, I:R.21 CDL.14: 7 residues within 4Å: Chain K: D.115 Chain T: L.184, S.209, T.211, L.214, L.272 Chain Y: N.390 3 PLIP interactions: 3 interactions with chain T Hydrophobic interactions: T:T.211 Hydrogen bonds: T:S.209, T:S.209 CDL.15: 14 residues within 4Å: Chain 0: F.166, W.167, K.169 Chain O: T.26, P.28, L.31, Y.32 Chain Q: L.337, P.338 Chain V: Y.24, K.28, R.32 Chain Y: T.55, F.121 12 PLIP interactions: 5 interactions with chain O, 1 interactions with chain Q, 4 interactions with chain V, 2 interactions with chain Y Hydrophobic interactions: O:L.31, O:Y.32, Q:L.337, Y:F.121, Y:F.121 Hydrogen bonds: O:T.26 Salt bridges: O:K.24, O:K.24, V:K.28, V:K.28, V:R.32, V:R.32

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

PEE.3: 10 residues within 4Å: Chain D: W.132 Chain Q: M.163, L.276, I.277, T.280, T.284 Chain Y: P.159, Y.166, A.191 Ligands: PEE.11 7 PLIP interactions: 3 interactions with chain Q, 4 interactions with chain Y Hydrophobic interactions: Q:L.276, Q:I.277, Q:T.284, Y:P.159, Y:Y.166 Hydrogen bonds: Y:Y.166, Y:Y.166 PEE.5: 17 residues within 4Å: Chain B: H.40 Chain E: F.112, M.113, Y.115, T.116 Chain R: F.3, A.4, L.7 Chain U: V.37, L.44, F.56, R.136 Chain Z: T.76, L.77, L.98, N.99, F.104 11 PLIP interactions: 4 interactions with chain R, 3 interactions with chain Z, 3 interactions with chain U, 1 interactions with chain E Hydrophobic interactions: R:F.3, R:F.3, R:A.4, R:L.7, Z:L.77, Z:F.104, U:L.44, U:F.56 Hydrogen bonds: Z:N.99, E:F.112 Salt bridges: U:R.136 PEE.11: 12 residues within 4Å: Chain A: Q.13, Y.20 Chain Q: I.285, L.288, Y.291, R.295 Chain T: P.563, S.567, Q.570, I.571 Chain Y: V.155 Ligands: PEE.3 12 PLIP interactions: 7 interactions with chain Q, 3 interactions with chain A, 2 interactions with chain Y Hydrophobic interactions: Q:I.285, Q:L.288, Q:Y.291, Q:Y.291, Y:V.155, Y:V.155 Hydrogen bonds: Q:Y.291, A:Q.13, A:Q.13, A:Y.20 Salt bridges: Q:R.295, Q:R.295 PEE.12: 15 residues within 4Å: Chain K: N.82, R.83 Chain T: T.166, Q.170, L.173, Y.174, M.533, H.534, I.537, P.538, G.541, T.544 Chain Y: S.274, L.277, L.405 11 PLIP interactions: 9 interactions with chain T, 2 interactions with chain Y Hydrophobic interactions: T:L.173, T:Y.174, T:I.537, T:P.538, Y:L.277, Y:L.405 Hydrogen bonds: T:T.166, T:Q.170, T:Q.170 Salt bridges: T:H.534, T:H.534

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

8Q1.16: 20 residues within 4Å: Chain F: D.40, S.41, L.42 Chain X: 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 X, 3 interactions with chain F Hydrophobic interactions: X:V.9, X:H.19, X:L.20, X:F.41, X:K.45, X:A.60, X:F.64, X:R.67 Hydrogen bonds: F:S.41, F:S.41, F:L.42

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] iron-sulfur protein 2, mitochondrial: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: E
Acyl carrier protein, mitochondrial: F
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial: G
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: H
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: I
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: L
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: M
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: N
NADH dehydrogenase [ubiquinone] 1 subunit C2: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: P
NADH-ubiquinone oxidoreductase chain 2: Q
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 4L: S
NADH-ubiquinone oxidoreductase chain 5: T
NADH-ubiquinone oxidoreductase chain 6: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: X
NADH-ubiquinone oxidoreductase chain 4: Y
NADH-ubiquinone oxidoreductase chain 1: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
S

C
U

D
V

E
W

F
X

G
Y

H
Z

I
a

J
b

K
c

L
d

M
e

N
f

O
g

P
h

Q
i

R
j

S
k

T
l

U
m

V
n

W
o

X
p

Y
r

Z
s

0
u

1
v

2
w

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

Acyl carrier protein, mitochondrial

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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