SMTL ID : 7p69.1

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Resting 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)(Covalent)

SF4.1: 13 residues within 4Å: Chain A: I.179, P.197, S.350, C.351, G.352, W.353, C.354, C.357, T.396, F.397, C.398, H.400, A.401 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.351, A:C.354, A:C.357, A:C.398 SF4.5: 12 residues within 4Å: Chain C: H.98, D.101, C.102, C.105, E.107, G.108, C.111, L.113, Q.114, T.202, G.203 Chain D: I.516 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.101 Metal complexes: C:H.98, C:C.102, C:C.105, C:C.111 SF4.6: 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 SF4.7: 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: 13 residues within 4Å: Chain D: R.254, R.274, H.359 Chain E: S.62, C.63, C.64, G.100, T.101, A.128, C.129, 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 SF4.11: 13 residues within 4Å: Chain F: I.13, C.35, P.36, V.37, C.39, I.40, C.64, I.65, F.66, C.67, G.68, L.69, C.70 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.35, F:C.64, F:C.67, F:C.70 SF4.12: 15 residues within 4Å: Chain F: L.15, C.25, V.26, A.27, C.28, N.29, L.30, C.31, L.42, F.57, C.74, P.75, T.76, A.78, I.79 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.25, F:C.28, F:C.31, F:C.74

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: G.61, R.62, G.63, K.72, N.90, D.92, E.93, M.94, Y.178, I.179, G.181, E.182, E.183, V.216, N.217, N.218, T.221, A.399, H.400 Ligands: NAI.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.178, A:I.179, A:E.182, A:A.399, A:H.400 Hydrogen bonds: A:G.63, A:N.90, A:N.90, A:E.93, A:M.94, A:G.181, A:E.182, A:E.183, A:N.217, A:N.218, A:T.221 Salt bridges: A:K.72

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

NAI.3: 16 residues within 4Å: Chain A: G.63, G.64, A.65, F.67, K.72, L.75, E.95, Y.178, E.182, E.183, K.200, F.203, R.320, T.323, A.399 Ligands: FMN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.95 Hydrogen bonds: A:E.95, A:E.183, A:R.320 Salt bridges: A:K.200, A:K.200 pi-Stacking: A:F.67, A:F.203

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

FES.4: 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 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.82, B:C.87, B:C.123, B:C.127 FES.8: 11 residues within 4Å: Chain C: Y.31, C.33, W.34, G.42, A.43, 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.9: 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

6 x LFA: EICOSANE(Non-covalent)

LFA.13: 8 residues within 4Å: Chain G: I.21, V.24, C.28, V.103, S.104, W.107, F.268, T.275 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.21, G:V.24, G:V.103, G:V.103, G:W.107, G:F.268, G:T.275 LFA.15: 8 residues within 4Å: Chain H: V.98, V.101, I.105 Chain K: I.3, L.15 Chain M: L.139, E.142, L.143 7 PLIP interactions: 2 interactions with chain H, 2 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: H:V.98, H:V.101, K:I.3, K:L.15, M:E.142, M:E.142, M:L.143 LFA.20: 2 residues within 4Å: Chain I: A.596 Chain M: G.95 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:A.596 LFA.24: 7 residues within 4Å: Chain I: G.39, T.87, S.90, G.94, F.97, F.340, I.471 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:F.97, I:F.97, I:F.97, I:F.340, I:I.471 LFA.28: 10 residues within 4Å: Chain J: F.115, W.122, L.156, W.157 Chain K: F.366, W.367, T.377, V.378, L.381, Y.433 13 PLIP interactions: 7 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:F.366, K:F.366, K:T.377, K:V.378, K:L.381, K:Y.433, K:Y.433, J:F.115, J:F.115, J:F.115, J:W.122, J:W.157, J:W.157 LFA.30: 7 residues within 4Å: Chain K: F.278, I.282, W.408, W.409, G.412 Ligands: 3PE.26, 3PE.27 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.278, K:I.282, K:I.282, K:W.408, K:W.409, K:W.409

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

3PE.14: 16 residues within 4Å: Chain G: I.89, D.111, L.112, N.113, I.114, F.118, M.122 Chain H: H.13, F.16, A.17, L.20, I.24 Chain M: L.37, F.44, Y.49 Ligands: 3PE.17 13 PLIP interactions: 4 interactions with chain G, 6 interactions with chain H, 3 interactions with chain M Hydrophobic interactions: G:I.89, G:L.112, G:I.114, H:F.16, H:F.16, H:A.17, H:L.20, H:I.24, M:L.37, M:F.44 Hydrogen bonds: G:N.113, M:Y.49 Salt bridges: H:H.13 3PE.16: 7 residues within 4Å: Chain G: K.303, P.307, I.311 Chain H: V.115, V.118, R.119 Chain K: L.26 7 PLIP interactions: 3 interactions with chain H, 3 interactions with chain G, 1 interactions with chain K Hydrophobic interactions: H:V.115, H:V.115, G:P.307, G:P.307, G:I.311, K:L.26 Hydrogen bonds: H:R.119 3PE.17: 14 residues within 4Å: Chain H: T.5, H.13 Chain M: M.1, F.3, A.4, I.7, C.8, I.11, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.14 9 PLIP interactions: 6 interactions with chain M, 3 interactions with chain H Hydrophobic interactions: M:F.3, M:A.4, M:I.11, M:L.37, M:F.44 Hydrogen bonds: M:M.1, H:T.5, H:T.5 Salt bridges: H:H.13 3PE.18: 17 residues within 4Å: Chain I: M.569, A.573, S.576, R.577 Chain J: K.165, T.169, I.176, Y.177, I.229, P.239, L.240 Chain K: L.289, V.416, A.419, I.420, Y.423 Ligands: 3PE.26 18 PLIP interactions: 6 interactions with chain K, 9 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: K:L.289, K:V.416, K:A.419, K:Y.423, K:Y.423, J:I.176, J:Y.177, J:I.229, J:I.229, J:P.239, I:R.577 Hydrogen bonds: K:Y.423, J:K.165, J:T.169, J:T.169 Salt bridges: J:K.165, I:R.577, I:R.577 3PE.19: 26 residues within 4Å: Chain I: L.12, A.19, F.20, R.22, G.23, R.115, Y.119, S.126, 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, L.477, F.480 Ligands: 3PE.23 22 PLIP interactions: 13 interactions with chain J, 9 interactions with chain I Hydrophobic interactions: J:W.383, J:A.386, J:L.389, J:L.389, J:F.390, J:F.390, J:F.390, J:V.472, J:V.473, J:V.476, J:L.477, J:F.480, I:L.12, I:L.12, I:F.20, I:L.141, I:L.148 Hydrogen bonds: J:W.378, I:R.22 Water bridges: I:E.111, I:G.112, I:R.115 3PE.21: 18 residues within 4Å: Chain I: A.165, M.168, K.169, V.172, V.173, V.176, L.235, Y.545, F.549, V.550, F.553, L.554 Chain J: F.306, F.427, V.434, H.441, R.442 Ligands: 3PE.25 16 PLIP interactions: 3 interactions with chain J, 13 interactions with chain I Hydrophobic interactions: J:F.427, J:V.434, I:M.168, I:K.169, I:V.172, I:V.173, I:V.176, I:Y.545, I:Y.545, I:F.549, I:F.549, I:F.549, I:V.550, I:F.553, I:F.553 Salt bridges: J:R.442 3PE.22: 16 residues within 4Å: Chain I: L.299, F.363, L.427, R.431, L.511, W.512, V.519, T.520, I.522, A.523, G.528, L.531, S.532, W.534, W.535, W.539 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:L.299, I:L.427, I:L.511, I:W.512, I:L.531, I:W.534, I:W.535, I:W.539 Salt bridges: I:R.431 3PE.23: 15 residues within 4Å: Chain I: I.8, I.9, L.12, I.13, V.16, L.64, W.65, T.66, F.77, V.129, L.141 Chain J: L.477, F.480, Y.481 Ligands: 3PE.19 18 PLIP interactions: 13 interactions with chain I, 5 interactions with chain J Hydrophobic interactions: I:I.8, I:I.9, I:L.12, I:L.12, I:I.13, I:W.65, I:W.65, I:W.65, I:W.65, I:F.77, I:F.77, I:V.129, I:L.141, J:F.480, J:Y.481, J:Y.481 Hydrogen bonds: J:Y.481, J:Y.481 3PE.25: 19 residues within 4Å: Chain I: F.180, I.187, M.214, W.217, L.220, M.221, L.223, G.224, L.233, P.234, V.286 Chain J: F.299, F.415, P.419, V.420, V.423, F.427, F.431 Ligands: 3PE.21 12 PLIP interactions: 7 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:F.299, J:V.420, J:V.423, J:V.423, J:F.427, J:F.427, J:F.431, I:F.180, I:W.217, I:L.220, I:L.223, I:V.286 3PE.26: 9 residues within 4Å: Chain J: S.216, G.218, L.225, F.228, I.229, L.293 Ligands: 3PE.18, 3PE.27, LFA.30 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:F.228, J:I.229, J:L.293 Hydrogen bonds: J:S.216, J:S.217, J:G.218 3PE.27: 15 residues within 4Å: Chain J: V.184, A.191, V.195, V.219, L.222, L.223, L.225, G.226, I.229 Chain K: H.406, W.408, V.411, G.412 Ligands: 3PE.26, LFA.30 18 PLIP interactions: 10 interactions with chain J, 8 interactions with chain K Hydrophobic interactions: J:V.184, J:V.184, J:A.191, J:V.195, 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:W.408, K:W.408, K:W.408, K:V.411 Salt bridges: K:H.406 3PE.29: 17 residues within 4Å: Chain K: L.49, W.53, G.56, Q.57, A.58, G.59, G.71, M.74, L.75, G.78, L.79, L.82, I.459, L.467, I.477, L.480, A.481 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:L.49, K:W.53, K:L.75, K:L.79, K:L.82, K:L.82, K:I.459, K:L.467, K:L.480, K:A.481 Water bridges: K:G.71

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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