SMTL ID : 6q9b.1

CI Membrane Arm focused refinement from Ovine respiratory SC I+III2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.1: 17 residues within 4Å: Chain B: M.1, L.3, M.4 Chain C: M.98, N.99, L.100, F.104 Chain D: G.38, G.42, L.45, N.46, S.50, L.54 Chain T: F.139, I.140, Y.142, T.143 9 PLIP interactions: 3 interactions with chain D, 1 interactions with chain T, 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:L.45, D:L.45, D:L.54, C:F.104, B:L.3 Hydrogen bonds: T:Y.142, C:N.99, C:N.99, C:L.100 3PE.3: 15 residues within 4Å: Chain F: D.163, T.166, L.169, Q.170, L.173, Y.174, M.533, H.534, T.537, P.538, N.541 Chain G: L.405 Chain Y: N.87, R.88, D.90 13 PLIP interactions: 9 interactions with chain F, 2 interactions with chain Y, 2 interactions with chain G Hydrophobic interactions: F:L.173, F:L.173, F:Y.174, F:T.537, F:P.538, G:L.405, G:L.405 Hydrogen bonds: F:D.163, F:Q.170, Y:D.90 Salt bridges: F:H.534, F:H.534, Y:R.88 3PE.4: 16 residues within 4Å: Chain A: Q.13, Y.14, M.19, Y.20 Chain F: I.566, S.567, Q.570 Chain G: L.147, Y.148, F.151, Y.152, L.212 Chain H: L.170, L.287, L.288, Y.291 11 PLIP interactions: 4 interactions with chain H, 1 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: H:L.170, H:L.287, H:L.288, H:Y.291, F:Q.570, G:Y.148, G:Y.148, G:F.151, G:F.151, G:Y.152, G:L.212 3PE.7: 12 residues within 4Å: Chain 1: L.26, N.30 Chain G: L.2, I.5, I.6, M.9, S.53, T.55, F.56, M.108 Chain R: P.29 Ligands: 3PE.12 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain 1 Hydrophobic interactions: G:L.2, G:I.5, G:I.6, 1:L.26 Hydrogen bonds: G:S.53, 1:N.30 3PE.12: 9 residues within 4Å: Chain 1: K.33 Chain L: F.168, W.169, T.170, M.171 Chain R: P.29, R.30, Y.33 Ligands: 3PE.7 6 PLIP interactions: 2 interactions with chain R, 3 interactions with chain L, 1 interactions with chain 1 Hydrophobic interactions: R:R.30, R:Y.33, L:F.168 Hydrogen bonds: L:W.169, L:M.171 Salt bridges: 1:K.33 3PE.13: 7 residues within 4Å: Chain F: W.557 Chain I: Y.107, G.108 Chain S: P.81, T.83, S.86 Ligands: CDL.5 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain S Hydrophobic interactions: F:W.557, F:W.557 Hydrogen bonds: S:P.81, S:S.86

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 14 residues within 4Å: Chain F: I.22, N.23, Q.116, K.119, Y.120, L.123, G.146, M.150 Chain G: A.357, L.360, L.369, L.442 Chain J: D.18, L.22 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.123, G:L.369, G:L.442 Hydrogen bonds: F:Q.116, F:Y.120 Salt bridges: F:K.119, F:K.119, F:K.119 CDL.5: 13 residues within 4Å: Chain F: I.561, T.565, A.569, K.572, M.573, T.576 Chain I: G.108, I.109, A.112, A.115, Y.116 Ligands: CDL.9, 3PE.13 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain I Hydrophobic interactions: F:I.561, F:T.565, F:K.572, F:T.576, I:A.115, I:Y.116 CDL.9: 14 residues within 4Å: Chain F: T.576, T.594 Chain H: F.113, L.160 Chain I: Y.38, S.39, L.42, K.43, Y.58, A.62, L.100, T.104, M.117 Ligands: CDL.5 11 PLIP interactions: 8 interactions with chain I, 1 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: I:Y.38, I:Y.38, I:Y.38, I:L.42, I:A.62, F:T.594, H:F.113, H:L.160 Hydrogen bonds: I:Y.58, I:T.104 Salt bridges: I:K.43 CDL.10: 16 residues within 4Å: Chain F: F.24 Chain J: V.37, I.40, T.41, N.44, V.45, E.49, H.69 Chain M: V.47, I.51 Chain U: W.79, Y.83, H.88 Chain Z: V.71, Y.79 Ligands: PC1.6 12 PLIP interactions: 5 interactions with chain J, 3 interactions with chain U, 2 interactions with chain M, 1 interactions with chain F, 1 interactions with chain Z Hydrophobic interactions: J:V.37, U:W.79, U:Y.83, M:V.47, F:F.24, Z:V.71 Hydrogen bonds: J:N.44, J:E.49, J:E.49, M:H.55 Salt bridges: J:H.69, U:H.88

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

PC1.6: 15 residues within 4Å: Chain F: W.66 Chain G: L.39, P.64, I.67, L.68, W.71, L.446, L.447, L.449, N.450 Chain Z: S.74, V.77, A.78, Y.79 Ligands: CDL.10 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain Z Hydrophobic interactions: G:L.39, G:I.67, G:W.71, G:L.446, G:L.447, G:N.450, Z:V.77 Hydrogen bonds: G:N.450 PC1.8: 8 residues within 4Å: Chain G: S.191, F.194, M.195, A.198 Chain H: I.276, I.277 Chain I: L.123, W.132 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: I:L.123, I:W.132, H:I.276, H:I.277, G:A.198 Hydrogen bonds: G:S.191

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

ZMP.11: 14 residues within 4Å: Chain K: D.43, S.44, L.45 Chain W: H.11, Q.12, V.15, R.46, F.47, H.50, K.51, A.59, L.62, L.63, A.66 6 PLIP interactions: 4 interactions with chain W, 2 interactions with chain K Hydrophobic interactions: W:F.47, W:K.51, W:A.66 Hydrogen bonds: W:Q.12, K:S.44, K:L.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Letts, J.A. et al., Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk. Mol.Cell (2019)

Release Date

2019-08-21

Peptides

NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2: 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
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: I
NADH:ubiquinone oxidoreductase subunit B5: J
Acyl carrier protein: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: L
NADH:ubiquinone oxidoreductase subunit B10: M
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: N
NADH:ubiquinone oxidoreductase subunit S5: O
NADH:ubiquinone oxidoreductase subunit A3: P
NADH:ubiquinone oxidoreductase subunit B3: Q
NADH dehydrogenase [ubiquinone] 1 subunit C2: R
NADH:ubiquinone oxidoreductase subunit B4: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: T
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: U
NADH:ubiquinone oxidoreductase subunit B7: V
NADH:ubiquinone oxidoreductase subunit B9: W
NADH:ubiquinone oxidoreductase subunit B2: X
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: Y
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: Z
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 0
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S2

B
D3

C
D1

D
D6

E
4L

F
D5

G
D4

H
D2

I
AK

J
B5

K
AB

L
A8

M
BJ

N
AJ

O
S5

P
A3

Q
B3

R
C2

S
B4

T
AM

U
B6

V
B7

W
B9

X
B2

Y
B8

Z
BK

0
C1

1
B1

2
A1

Membrane

We predict this structure to be a membrane protein.
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NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2

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:ubiquinone oxidoreductase subunit B5

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH:ubiquinone oxidoreductase subunit B10

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

NADH:ubiquinone oxidoreductase subunit S5

NADH:ubiquinone oxidoreductase subunit A3

NADH:ubiquinone oxidoreductase subunit B3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

NADH:ubiquinone oxidoreductase subunit B2

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

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

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

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