SMTL ID : 7p64.1

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, 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 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.348, A:C.351, A:C.354, A:C.395 SF4.5: 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 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: 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: 15 residues within 4Å: Chain F: L.50, C.60, V.61, A.62, C.63, N.64, L.65, C.66, L.77, F.92, C.109, P.110, T.111, A.113, 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: 20 residues within 4Å: Chain A: G.58, R.59, G.60, K.69, N.87, D.89, E.90, M.91, Y.175, I.176, G.178, E.179, E.180, V.213, N.214, N.215, T.218, A.396, H.397 Ligands: NAI.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.175, A:I.176, A:E.179, A:A.396, A:H.397 Hydrogen bonds: A:G.60, A:N.87, A:N.87, A:E.90, A:M.91, A:G.178, A:E.180, A:N.214, A:N.215, A:T.218 Salt bridges: A:K.69

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

NAI.3: 16 residues within 4Å: Chain A: G.60, G.61, A.62, F.64, K.69, L.72, E.92, Y.175, E.179, E.180, K.197, F.200, R.317, T.320, A.396 Ligands: FMN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.92 Hydrogen bonds: A:K.69, A:E.92, A:E.179, A:E.179, A:E.180 Salt bridges: A:K.197, A:K.197 pi-Stacking: A:F.64, A:F.200

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: 10 residues within 4Å: Chain C: Y.31, C.33, W.34, G.42, A.43, C.44, R.45, 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

1 x DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione(Non-covalent)

DCQ.11: 10 residues within 4Å: Chain D: Q.328 Chain E: W.55, F.72, E.84, V.85, L.86 Chain G: R.37, F.238, Y.242, R.286 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:W.55, G:F.238

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

3PE.14: 16 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, I.201, L.308 Ligands: 3PE.15, 3PE.16, 3PE.19, 3PE.21 Ligand excluded by PLIP 3PE.15: 6 residues within 4Å: Chain D: K.396 Chain F: V.14, R.15, W.18, M.19 Ligands: 3PE.14 Ligand excluded by PLIP 3PE.16: 28 residues within 4Å: Chain D: T.402, I.403, G.406 Chain F: M.1, E.5, L.6, G.9, F.10, Q.13, V.14 Chain G: F.196, A.200, I.201, V.204, F.212, I.248, 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 Ligand excluded by PLIP 3PE.18: 6 residues within 4Å: Chain G: A.184, H.185, V.186, W.187, F.257, P.263 Ligand excluded by PLIP 3PE.19: 16 residues within 4Å: Chain G: Q.170, I.190, P.191, Q.192, F.194, L.308, I.311, N.312, V.315, T.316, V.319, I.320, Q.323 Chain H: R.93 Ligands: 3PE.14, 3PE.21 Ligand excluded by PLIP 3PE.20: 16 residues within 4Å: Chain G: I.89, D.111, L.112, N.113, I.114, F.118, M.122, L.125 Chain H: H.13, F.16, A.17, L.20, I.24 Chain M: F.44, Y.49 Ligands: 3PE.36 Ligand excluded by PLIP 3PE.21: 15 residues within 4Å: Chain F: M.1, L.3, L.6 Chain G: K.303, I.304, P.307, L.308 Chain H: F.108, L.111, V.115, V.118, R.119 Chain K: L.26 Ligands: 3PE.14, 3PE.19 Ligand excluded by PLIP 3PE.22: 18 residues within 4Å: Chain I: M.569, P.572, A.573, R.577 Chain J: T.169, I.176, Y.177, S.181, I.229, V.233, L.240 Chain K: L.289, V.416, A.419, I.420, Y.423 Ligands: 3PE.29, 3PE.30 Ligand excluded by PLIP 3PE.23: 25 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.476, L.477, F.480 Ligands: 3PE.27 Ligand excluded by PLIP 3PE.25: 18 residues within 4Å: Chain I: 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.427, A.438, H.441, R.442 Ligands: 3PE.31 Ligand excluded by PLIP 3PE.26: 17 residues within 4Å: Chain I: F.296, L.299, F.363, V.420, L.427, R.431, L.511, W.512, V.519, I.522, A.523, G.528, L.531, S.532, W.535, W.539 Ligands: 3PE.28 Ligand excluded by PLIP 3PE.27: 15 residues within 4Å: Chain I: I.8, L.12, V.16, L.64, W.65, T.66, F.77, V.129, L.141 Chain J: V.476, L.477, F.480, Y.481 Ligands: 3PE.23, LFA.32 Ligand excluded by PLIP 3PE.28: 11 residues within 4Å: Chain I: L.233, H.281, I.285, V.289, L.292, L.293, F.296, H.411, N.413, L.414 Ligands: 3PE.26 Ligand excluded by PLIP 3PE.29: 13 residues within 4Å: Chain J: S.216, S.217, G.218, V.219, L.222, L.225, F.228, L.240, F.286, L.293 Ligands: 3PE.22, 3PE.30, LFA.34 Ligand excluded by PLIP 3PE.30: 19 residues within 4Å: Chain J: V.184, V.195, M.215, S.216, V.219, L.222, L.223, L.225, G.226, I.229 Chain K: H.406, W.408, V.411, G.412, V.415, V.416 Ligands: 3PE.22, 3PE.29, LFA.34 Ligand excluded by PLIP 3PE.31: 15 residues within 4Å: Chain I: I.187, M.214, W.217, L.220, M.221, V.227, P.234 Chain J: F.299, F.415, P.419, V.420, V.423, I.424, F.427 Ligands: 3PE.25 Ligand excluded by PLIP 3PE.35: 8 residues within 4Å: Chain K: L.19, T.20, N.33, F.35, L.36, L.40, I.43, A.47 Ligand excluded by PLIP 3PE.36: 13 residues within 4Å: Chain H: H.13 Chain M: M.1, F.3, A.4, I.7, I.11, I.34, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.20 Ligand excluded by PLIP

5 x LFA: EICOSANE(Non-covalent)

LFA.17: 9 residues within 4Å: Chain G: I.21, V.24, V.25, C.28, V.103, S.104, W.107, F.268, I.269 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.21, G:V.25, G:V.103, G:W.107, G:F.268, G:F.268, G:I.269 LFA.24: 7 residues within 4Å: Chain I: Y.590, R.592, A.596 Chain L: D.93 Chain M: G.95, L.99, I.102 5 PLIP interactions: 2 interactions with chain M, 3 interactions with chain I Hydrophobic interactions: M:L.99, M:I.102, I:Y.590, I:Y.590, I:A.596 LFA.32: 9 residues within 4Å: Chain J: L.89, V.92, L.474, L.477, L.478, Y.481, P.484, I.485 Ligands: 3PE.27 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.92, J:L.477, J:L.477, J:L.478, J:Y.481, J:P.484 LFA.33: 12 residues within 4Å: Chain J: Y.112, F.115, W.157 Chain K: F.366, W.367, A.374, L.381, P.387, M.388, T.389, Y.433, L.465 14 PLIP interactions: 6 interactions with chain J, 8 interactions with chain K Hydrophobic interactions: J:Y.112, J:F.115, J:F.115, J:F.115, J:F.115, J:W.157, K:F.366, K:F.366, K:W.367, K:A.374, K:M.388, K:T.389, K:Y.433, K:L.465 LFA.34: 7 residues within 4Å: Chain K: F.278, W.408, W.409, G.412, V.416 Ligands: 3PE.29, 3PE.30 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.278, K:W.409, 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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