SMTL ID : 9q8i.1

Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.35 Å

Oligo State

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

Ligands

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

3PE.1: 12 residues within 4Å: Chain A: H.13, F.16, A.17, L.20 Chain G: D.111, L.112, N.113, I.114, F.118 Chain I: F.44, Y.49 Ligands: 3PE.14 11 PLIP interactions: 3 interactions with chain G, 4 interactions with chain A, 4 interactions with chain I Hydrophobic interactions: G:I.114, G:F.118, A:F.16, A:F.16, A:A.17, I:F.44, I:F.44 Hydrogen bonds: G:N.113, I:Y.49, I:Y.49 Salt bridges: A:H.13 3PE.14: 13 residues within 4Å: Chain A: H.13 Chain I: M.1, A.4, I.7, C.8, I.11, I.34, L.37, A.38, G.41, F.44, S.45 Ligands: 3PE.1 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:I.7, I:I.11, I:I.34, I:F.44 Hydrogen bonds: I:M.1 Salt bridges: A:H.13 3PE.15: 9 residues within 4Å: Chain K: I.9, L.12, I.13, L.64, W.65, T.66 Chain L: L.477, F.480, Y.481 17 PLIP interactions: 10 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:I.9, K:L.12, K:L.12, K:I.13, K:W.65, K:W.65, K:W.65, K:W.65, K:W.65, L:L.477, L:F.480, L:F.480, L:F.480, L:Y.481, L:Y.481 Hydrogen bonds: K:T.66, L:Y.481 3PE.16: 22 residues within 4Å: Chain K: M.569, N.570, A.573, S.576, R.577 Chain L: K.165, T.169, K.173, I.176, Y.177, A.180, S.181, V.184, I.229, V.233, L.240 Chain M: L.289, V.415, A.419, I.420, Y.423 Ligands: 3PE.21 17 PLIP interactions: 10 interactions with chain L, 5 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: L:K.173, L:K.173, L:Y.177, L:Y.177, L:A.180, L:V.184, L:I.229, L:V.233, L:L.240, M:L.289, M:V.415, M:A.419, M:Y.423, M:Y.423, K:R.577 Salt bridges: L:K.165, K:R.577 3PE.17: 19 residues within 4Å: Chain K: A.165, M.168, V.172, V.176, L.235, Y.545, F.549, V.550, F.553, L.554 Chain L: F.306, F.427, V.430, F.431, V.434, A.438, H.441, R.442 Ligands: 3PE.19 20 PLIP interactions: 8 interactions with chain L, 12 interactions with chain K Hydrophobic interactions: L:F.427, L:F.427, L:V.430, L:F.431, L:V.434, L:V.434, K:M.168, K:V.176, K:V.176, K:L.235, K:Y.545, K:Y.545, K:F.549, K:F.549, K:F.549, K:F.549, K:F.553, K:L.554 Hydrogen bonds: L:H.441 Salt bridges: L:R.442 3PE.18: 22 residues within 4Å: Chain K: F.15, A.19, F.20, R.22, R.115, Y.119, S.126, V.129 Chain L: W.378, K.382, W.383, A.386, L.387, L.389, F.390, V.393, P.399, V.472, V.473, V.476, L.477, F.480 9 PLIP interactions: 3 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:F.20, K:F.20, K:V.129, L:L.387, L:V.393, L:V.472, L:V.476, L:V.476, L:F.480 3PE.19: 13 residues within 4Å: Chain K: F.180, F.183, I.187, M.214, W.217, M.221 Chain L: F.299, F.415, P.419, V.423, I.424, F.427 Ligands: 3PE.17 12 PLIP interactions: 7 interactions with chain L, 5 interactions with chain K Hydrophobic interactions: L:F.299, L:V.423, L:V.423, L:F.427, L:F.427, L:F.427, L:F.427, K:F.180, K:F.183, K:I.187, K:W.217 Hydrogen bonds: K:E.191 3PE.20: 8 residues within 4Å: Chain L: G.218, Y.221, L.222, F.228, E.285, F.286, I.289, L.293 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:Y.221, L:F.228, L:F.286, L:I.289, L:L.293 3PE.21: 16 residues within 4Å: Chain L: V.184, A.188, A.191, V.195, V.219, L.222, L.223, L.225, G.226, I.229 Chain M: H.406, W.408, V.411, G.412, V.415 Ligands: 3PE.16 14 PLIP interactions: 7 interactions with chain M, 7 interactions with chain L Hydrophobic interactions: M:W.408, M:W.408, M:W.408, M:V.411, M:V.415, L:V.184, L:A.188, L:A.191, L:L.222, L:L.222, L:L.225, L:I.229 Salt bridges: M:H.406, M:H.406 3PE.22: 15 residues within 4Å: Chain M: L.49, V.50, L.52, W.53, G.56, Q.57, G.59, M.74, L.75, G.78, F.335, L.463, L.467, I.477, A.481 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:L.52, M:W.53, M:W.53, M:W.53, M:M.74, M:L.75, M:F.335, M:L.463, M:L.467, M:A.481

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

SF4.2: 13 residues within 4Å: Chain B: S.62, C.63, C.64, G.100, T.101, G.127, A.128, C.129, Y.136, C.158, P.159 Chain C: R.250, H.355 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.63, B:C.64, B:C.129, B:C.158 SF4.4: 12 residues within 4Å: Chain E: I.195, P.213, S.366, C.367, G.368, W.369, C.370, C.373, T.412, F.413, C.414, H.416 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.367, E:C.370, E:C.373, E:C.414 SF4.6: 12 residues within 4Å: Chain C: I.512 Chain F: H.99, D.102, C.103, C.106, E.108, G.109, C.112, L.114, Q.115, T.203, G.204 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:D.102 Metal complexes: F:H.99, F:C.103, F:C.106, F:C.112 SF4.7: 13 residues within 4Å: Chain F: C.151, I.152, A.153, C.154, Y.155, R.156, C.157, F.181, C.201, P.202, T.203, V.205, F.206 5 PLIP interactions: 5 interactions with chain F, pi-Cation interactions: F:F.181 Metal complexes: F:C.151, F:C.154, F:C.157, F:C.201 SF4.8: 8 residues within 4Å: Chain F: C.228, Q.230, C.231, I.233, G.234, C.235, C.263, R.388 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.228, F:C.231, F:C.235, F:C.263 SF4.12: 14 residues within 4Å: Chain H: 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, L.116 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.70, H:C.99, H:C.102, H:C.105 SF4.13: 13 residues within 4Å: Chain H: 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 H, Metal complexes: H:C.60, H:C.63, H:C.66, H:C.109

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

FES.3: 10 residues within 4Å: Chain D: C.92, S.94, P.96, C.97, C.133, L.134, G.135, N.136, C.137, M.142 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.92, D:C.97, D:C.133, D:C.137 FES.9: 10 residues within 4Å: Chain F: Y.32, F.33, C.34, W.35, G.43, A.44, C.45, R.46, C.48, C.67 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.34, F:C.45, F:C.48, F:C.67

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 18 residues within 4Å: Chain E: G.77, R.78, G.79, K.88, N.106, D.108, E.109, M.110, Y.194, G.197, E.198, E.199, V.232, N.233, N.234, T.237, A.415, H.416 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:Y.194, E:Y.194, E:E.198, E:E.198, E:A.415, E:H.416 Hydrogen bonds: E:R.78, E:G.79, E:N.106, E:D.108, E:D.108, E:M.110, E:G.197, E:E.199, E:N.233, E:N.234, E:N.234 Salt bridges: E:K.88

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain F: D.617, Q.632, E.647, D.731 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.617, F:D.617, F:E.647, F:D.731

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain F: G.474, R.802 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain M: R.369, I.371 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wohlwend, D. et al., Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I. To Be Published

Release Date

2025-11-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
H

H
I

I
J

J
K

K
L

L
M

M
N

Membrane

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

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit C/D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

NADH-quinone oxidoreductase subunit G

NADH-quinone oxidoreductase subunit H

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit J

NADH-quinone oxidoreductase subunit K

NADH-quinone oxidoreductase subunit L

NADH-quinone oxidoreductase subunit M

NADH-quinone oxidoreductase subunit N

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