SMTL ID : 7p7l.1

Complex I from E. coli, DDM/LMNG-purified, with NADH and FMN, Open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.176, P.194, S.347, C.348, G.349, W.350, C.351, C.354, T.393, F.394, C.395, H.397, A.398 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.348, A:C.351, A:C.354 SF4.4: 13 residues within 4Å: Chain C: H.98, D.101, C.102, C.105, E.107, G.108, C.111, L.113, Q.114, R.149, T.202, G.203 Chain D: I.516 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.98, C:C.102, C:C.105, C:C.111 SF4.5: 13 residues within 4Å: Chain C: C.150, I.151, A.152, C.153, Y.154, R.155, C.156, F.180, C.200, P.201, T.202, V.204, F.205 5 PLIP interactions: 5 interactions with chain C, pi-Cation interactions: C:F.180 Metal complexes: C:C.150, C:C.153, C:C.156, C:C.200 SF4.6: 11 residues within 4Å: Chain C: C.227, Q.229, C.230, I.232, G.233, C.234, L.261, C.262, R.264, G.265, R.387 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.227, C:C.230, C:C.234, C:C.262 SF4.10: 15 residues within 4Å: Chain D: R.254, R.274, H.359 Chain E: S.62, C.63, C.64, G.100, T.101, G.127, A.128, C.129, Y.136, G.157, C.158, P.159 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.63, E:C.64, E:C.129, E:C.158 SF4.12: 13 residues within 4Å: Chain F: I.48, C.70, P.71, V.72, C.74, I.75, C.99, I.100, F.101, C.102, G.103, L.104, C.105 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.70, F:C.99, F:C.102, F:C.105 SF4.13: 13 residues within 4Å: Chain F: C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, F.92, C.109, P.110, T.111, I.114 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.60, F:C.63, F:C.66, F:C.109

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.58, R.59, G.60, A.62, K.69, N.87, D.89, E.90, M.91, E.92, Y.175, G.178, E.179, E.180, V.213, N.214, N.215, T.218, H.397 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.179, A:H.397 Hydrogen bonds: A:R.59, A:G.60, A:A.62, A:N.87, A:N.87, A:E.90, A:M.91, A:E.92, A:G.178, A:N.215, A:T.218 Salt bridges: A:K.69

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

FES.3: 10 residues within 4Å: Chain B: C.82, S.84, V.86, C.87, C.123, L.124, G.125, N.126, C.127, N.132 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.82, B:C.87 FES.7: 11 residues within 4Å: Chain C: L.19, Y.31, C.33, W.34, G.42, C.44, R.45, Q.46, C.47, M.64, C.66 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.33, C:C.44, C:C.47, C:C.66

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain C: D.616, Q.631, E.646, D.728, D.730 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.616, C:E.646, C:D.730

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

3PE.9: 28 residues within 4Å: Chain D: T.402, I.403, G.406, Q.409 Chain F: M.1, E.5, L.6, G.9, F.10, Q.13, V.14 Chain G: F.196, I.201, V.204, F.212, S.249, M.252, F.278, M.281, F.282, I.285, L.289, P.292, Q.296, V.297, F.300 Ligands: 3PE.14, 3PE.16 18 PLIP interactions: 2 interactions with chain D, 11 interactions with chain G, 5 interactions with chain F Hydrogen bonds: D:T.402, D:G.406, G:Q.296 Hydrophobic interactions: G:F.196, G:I.201, G:F.212, G:F.212, G:F.278, G:M.281, G:F.282, G:L.289, G:P.292, G:F.300, F:L.6, F:F.10, F:F.10, F:Q.13, F:V.14 3PE.14: 15 residues within 4Å: Chain F: L.6, L.7, V.8, F.10, G.11, T.12, V.14, R.15 Chain G: F.193, I.197, F.300, L.308 Ligands: 3PE.9, 3PE.16, 3PE.17 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:L.6, F:L.7, F:L.7, F:F.10, F:V.14, G:F.193, G:F.300, G:L.308 Salt bridges: F:R.15, F:R.15 3PE.16: 13 residues within 4Å: Chain G: A.184, H.185, V.186, W.187, V.189, F.193, F.196, G.262, P.263, W.270, F.277 Ligands: 3PE.9, 3PE.14 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:W.187, G:W.187, G:V.189, G:F.193, G:F.196, G:F.196, G:W.270, G:F.277, G:F.277 Hydrogen bonds: G:W.187 Salt bridges: G:H.185 3PE.17: 15 residues within 4Å: Chain G: Q.170, I.190, P.191, Q.192, F.193, F.194, L.308, I.311, N.312, V.315, T.316, V.319, Q.323 Chain H: R.93 Ligands: 3PE.14 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:I.190, G:P.191, G:P.191, G:F.193, G:F.194, G:F.194, G:I.311, G:I.311, G:V.315, G:V.319 Hydrogen bonds: G:Q.192, G:Q.323 Salt bridges: H:R.93 3PE.18: 19 residues within 4Å: Chain G: I.89, L.96, D.111, L.112, N.113, I.114, F.118, L.125 Chain H: V.9, H.13, F.16, A.17, L.20, I.24 Chain M: I.33, L.37, F.44, Y.49 Ligands: 3PE.20 20 PLIP interactions: 8 interactions with chain G, 8 interactions with chain H, 4 interactions with chain M Hydrophobic interactions: G:I.89, G:L.96, G:L.112, G:I.114, G:F.118, G:L.125, H:F.16, H:F.16, H:A.17, H:L.20, H:L.20, H:I.24, M:I.33, M:L.37, M:F.44 Hydrogen bonds: G:N.113, G:N.113, M:Y.49 Salt bridges: H:H.13, H:H.13 3PE.19: 9 residues within 4Å: Chain G: K.303, P.307, I.311 Chain H: F.108, L.111, V.115, V.118, R.119, D.124 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:F.108, H:L.111, H:V.115, H:V.118, G:P.307, G:I.311 Hydrogen bonds: H:R.119 Salt bridges: H:R.119, H:R.119 3PE.20: 14 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, C.8, I.11, I.34, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.18 7 PLIP interactions: 6 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: M:F.3, M:A.4, M:I.7, M:I.11, M:L.37, M:F.44 Salt bridges: H:H.13 3PE.21: 26 residues within 4Å: Chain I: L.12, A.19, R.22, G.23, R.115, Y.119, L.122, S.126, V.129, L.141, G.145, L.148 Chain J: W.378, M.381, K.382, W.383, A.386, L.389, F.390, M.398, P.399, V.472, V.473, V.476, F.480 Ligands: 3PE.25 15 PLIP interactions: 9 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:W.383, J:A.386, J:L.389, J:V.472, J:V.473, J:V.476, J:V.476, J:F.480, I:L.12, I:L.12, I:L.122, I:V.129, I:L.141, I:L.148 Hydrogen bonds: J:W.378 3PE.23: 21 residues within 4Å: Chain I: A.165, M.168, K.169, V.172, V.173, V.176, F.180, P.234, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, F.431, A.438, H.441, R.442 Ligands: 3PE.30 14 PLIP interactions: 10 interactions with chain I, 4 interactions with chain J Hydrophobic interactions: I:K.169, I:V.173, I:V.176, I:F.180, I:P.234, I:F.549, I:F.549, I:V.550, I:V.550, I:F.553, J:F.306, J:F.427, J:F.431 Salt bridges: J:R.442 3PE.24: 12 residues within 4Å: Chain I: L.299, F.363, R.431, L.511, W.512, V.519, I.522, A.523, G.528, L.531, S.532, W.535 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:L.299, I:L.511, I:W.512, I:I.522, I:L.531, I:W.535, I:W.535 Salt bridges: I:R.431 3PE.25: 17 residues within 4Å: Chain I: I.8, L.12, I.13, F.15, V.16, L.64, W.65, T.66, F.77, V.129, L.141 Chain J: L.477, F.480, Y.481, Q.483 Ligands: 3PE.21, LFA.27 21 PLIP interactions: 14 interactions with chain I, 7 interactions with chain J Hydrophobic interactions: I:I.8, I:L.12, I:L.12, I:I.13, I:F.15, I:V.16, I:W.65, I:W.65, I:W.65, I:F.77, I:F.77, I:V.129, I:L.141, J:L.477, J:F.480, J:F.480, J:F.480, J:Y.481 Hydrogen bonds: I:T.66, J:Y.481, J:Y.481 3PE.26: 17 residues within 4Å: Chain I: M.569, A.573, S.576, R.577 Chain J: T.169, I.176, Y.177, S.181, I.229, P.239, L.240 Chain K: L.289, V.416, A.419, Y.423 Ligands: 3PE.28, 3PE.29 13 PLIP interactions: 6 interactions with chain K, 5 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: K:L.289, K:V.416, K:A.419, K:Y.423, J:I.176, J:Y.177, J:I.229, J:P.239 Hydrogen bonds: K:Y.423, K:Y.423, J:T.169 Salt bridges: I:R.577, I:R.577 3PE.28: 13 residues within 4Å: Chain I: S.576 Chain J: S.216, S.217, G.218, Y.221, L.222, L.225, I.229, L.240, L.293 Ligands: 3PE.26, 3PE.29, LFA.32 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:Y.221, J:L.222, J:L.225, J:L.225, J:I.229, J:L.240, J:L.293 Hydrogen bonds: J:S.217 3PE.29: 19 residues within 4Å: Chain J: V.184, I.187, A.191, V.195, M.215, S.216, V.219, L.222, L.223, L.225, G.226, I.229 Chain K: H.406, W.408, G.412, V.415 Ligands: 3PE.26, 3PE.28, LFA.32 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain K Hydrophobic interactions: J:V.184, J:I.187, J:A.191, J:V.219, J:L.222, J:L.222, J:L.223, J:L.225, J:I.229, K:W.408, K:W.408, K:W.408, K:V.415 Hydrogen bonds: J:S.216 Salt bridges: K:H.406 3PE.30: 17 residues within 4Å: Chain I: F.180, I.187, M.214, W.217, L.220, L.223, G.224, V.227 Chain J: F.299, W.303, F.415, P.419, V.420, V.423, I.424, F.427 Ligands: 3PE.23 15 PLIP interactions: 6 interactions with chain I, 9 interactions with chain J Hydrophobic interactions: I:F.180, I:I.187, I:W.217, I:L.220, I:L.223, I:V.227, J:F.299, J:F.299, J:F.299, J:W.303, J:W.303, J:F.415, J:I.424, J:F.427, J:F.427

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.11: 14 residues within 4Å: Chain D: Q.328, F.337 Chain E: N.58, E.84, V.85, L.86 Chain G: E.36, R.37, D.63, M.67, F.238, V.239, Y.242, R.286 8 PLIP interactions: 6 interactions with chain G, 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: G:R.37, G:D.63, G:F.238, G:F.238, G:F.238, G:V.239, E:V.85 Hydrogen bonds: D:Q.328

5 x LFA: EICOSANE(Non-covalent)

LFA.15: 6 residues within 4Å: Chain G: V.20, I.21, V.24, V.103, W.107, F.268 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:V.20, G:I.21, G:V.24, G:V.103, G:W.107, G:W.107, G:F.268, G:F.268, G:F.268, G:F.268 LFA.22: 5 residues within 4Å: Chain I: Y.590, R.592, A.596 Chain M: G.95, L.99 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain M Hydrophobic interactions: I:Y.590, I:Y.590, I:A.596, M:L.99 LFA.27: 6 residues within 4Å: Chain J: V.92, L.474, L.478, Y.481, I.485 Ligands: 3PE.25 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.92, J:L.474, J:L.478, J:Y.481, J:Y.481, J:I.485 LFA.31: 14 residues within 4Å: Chain J: Y.112, F.115, L.156, W.157, K.160 Chain K: F.366, W.367, A.374, T.377, V.378, L.381, M.388, Y.433, L.465 14 PLIP interactions: 7 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:Y.112, J:F.115, J:F.115, J:F.115, J:F.115, J:W.157, J:W.157, K:F.366, K:F.366, K:W.367, K:T.377, K:V.378, K:Y.433, K:L.465 LFA.32: 7 residues within 4Å: Chain K: F.278, W.408, W.409, G.412, V.416 Ligands: 3PE.28, 3PE.29 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.278, K:W.408, K:W.409, K:V.416

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-quinone oxidoreductase subunit F: A
NADH dehydrogenase I subunit E: B
NADH-quinone oxidoreductase: C
NADH-quinone oxidoreductase subunit C/D: D
NADH-quinone oxidoreductase subunit B: E
NADH-quinone oxidoreductase subunit I: F
NADH-quinone oxidoreductase subunit H: G
NADH-quinone oxidoreductase subunit A: H
Proton-translocating NADH-quinone oxidoreductase, chain L: I
NADH dehydrogenase I subunit M: J
NADH-quinone oxidoreductase subunit N: K
NADH-quinone oxidoreductase subunit K: L
NADH-quinone oxidoreductase subunit J: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

C
G

D
C

E
B

F
I

G
H

H
A

I
L

J
M

K
N

L
K

M
J

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit F

NADH dehydrogenase I subunit E

NADH-quinone oxidoreductase

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit A

Proton-translocating NADH-quinone oxidoreductase, chain L

NADH dehydrogenase I subunit M

NADH-quinone oxidoreductase subunit N

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit J

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