SMTL ID : 6zk9.1

Peripheral domain of open complex I during turnover

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-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, I.424, C.425, L.427 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.379, A:C.382, A:C.385, A:C.425 SF4.5: 14 residues within 4Å: Chain C: H.124, P.125, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 Chain D: M.375, I.379 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C, pi-Cation interactions: D:F.382 Salt bridges: C:D.127 Metal complexes: C:H.124, C:C.128, C:C.131, C:C.137 SF4.6: 14 residues within 4Å: Chain C: M.173, C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, C.226, P.227, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.176, C:C.179, C:C.182, C:C.226 SF4.9: 15 residues within 4Å: Chain D: R.118, R.138, H.223 Chain F: A.97, C.98, C.99, G.134, T.135, G.161, S.162, C.163, Y.170, G.192, C.193, P.194 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.98, F:C.99, F:C.163, F:C.193 SF4.13: 12 residues within 4Å: Chain G: H.106, C.128, P.129, I.133, C.157, I.158, Y.159, C.160, G.161, F.162, C.163, E.174 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.174 Metal complexes: G:C.128, G:C.157, G:C.163 SF4.14: 14 residues within 4Å: Chain G: C.118, I.119, A.120, C.121, K.122, L.123, C.124, I.135, Y.150, C.167, P.168, V.169, A.171, I.172 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.118, G:C.121, G:C.124, G:C.167

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: G.87, R.88, G.89, K.98, N.116, D.118, E.119, G.120, Y.204, I.205, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 Ligands: NAI.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.204, A:I.205, A:E.208, A:E.208, A:A.426, A:L.427 Hydrogen bonds: A:G.89, A:G.90, A:N.116, A:E.119, A:G.120, A:G.207, A:G.207, A:E.209, A:N.244 Water bridges: A:G.92, A:G.92, A:K.98, A:K.98, A:N.116, A:G.207, A:G.207, A:N.244, A:N.244, A:N.244 Salt bridges: A:K.98

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

NAI.3: 18 residues within 4Å: Chain A: G.89, G.90, A.91, F.93, K.98, F.101, E.119, G.120, E.121, Y.204, E.209, K.226, F.229, S.323, G.350, T.351, A.426 Ligands: FMN.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.121, A:Y.204, A:T.351 Hydrogen bonds: A:G.89, A:K.98, A:G.120, A:E.121, A:E.209, A:K.226, A:S.323, A:S.323 Water bridges: A:K.98, A:K.98, A:N.244, A:T.351, A:A.426 Salt bridges: A:K.226, A:K.226 pi-Stacking: A:F.93, A:F.229

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

FES.4: 10 residues within 4Å: Chain B: C.132, T.134, P.136, C.137, C.173, L.174, G.175, A.176, C.177, M.182 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.137, B:C.173, B:C.177 FES.7: 9 residues within 4Å: Chain C: R.62, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.64, C:C.75, C:C.78, C:C.92

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain C: Q.133, I.223, C.226, V.228, L.231 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:I.223, C:C.226, C:V.228, C:L.231

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

PC1.10: 8 residues within 4Å: Chain F: I.81, R.85, R.216, L.217, W.220, R.223 Chain K: D.90 Ligands: 3PE.11 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: F:I.81, F:I.81, F:L.217, F:W.220 Water bridges: F:R.216, F:R.223 Salt bridges: F:R.223, K:D.90 PC1.12: 7 residues within 4Å: Chain D: R.266 Chain G: T.65, L.66, W.68, L.71, L.75 Chain R: F.36 7 PLIP interactions: 1 interactions with chain R, 2 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: R:F.36, G:W.68, G:L.71, G:L.71, G:L.75 Salt bridges: D:R.266, D:R.266

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

3PE.11: 11 residues within 4Å: Chain F: Y.72, V.73, D.79, L.80, W.83, R.86, K.212 Chain P: W.75, D.76 Ligands: PC1.10, 3PE.19 14 PLIP interactions: 2 interactions with chain P, 12 interactions with chain F Hydrogen bonds: P:R.29 Water bridges: P:N.31 Hydrophobic interactions: F:Y.72, F:V.73, F:D.79, F:L.80, F:W.83, F:W.83, F:W.83, F:W.83 Salt bridges: F:R.86, F:R.86, F:K.212, F:K.212 3PE.19: 4 residues within 4Å: Chain P: F.28, F.74, W.75 Ligands: 3PE.11 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 5 residues within 4Å: Chain I: C.87, G.89, H.96, C.112, C.115 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.87, I:H.96, I:C.112, I:C.115

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.16: 26 residues within 4Å: Chain F: R.223 Chain K: G.60, A.61, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, V.130, G.131, R.132, F.139, V.144, F.145, I.148, I.167, S.168, H.169, Y.180, K.184, P.203, I.206, R.212 34 PLIP interactions: 33 interactions with chain K, 1 interactions with chain F Hydrophobic interactions: K:P.203, K:I.206, K:I.206 Hydrogen bonds: K:G.60, K:T.62, K:T.62, K:T.62, K:F.64, K:L.65, K:R.85, K:R.85, K:L.129, K:G.131, K:K.184, K:I.206, K:I.206 Water bridges: K:G.63, K:G.66, K:R.85, K:C.86, K:V.130, K:R.132, K:R.132, K:E.133, K:E.133, K:R.212 Salt bridges: K:R.85, K:R.132, K:R.132, K:R.212, K:R.212, F:R.223 pi-Cation interactions: K:R.85, K:R.85

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

ZMP.17: 18 residues within 4Å: Chain N: M.37, K.41, V.44, L.47, W.51, K.74, V.75, M.78, F.79, N.82, A.83, V.85, V.91, L.94, F.118 Chain Q: D.112, S.113, L.114 19 PLIP interactions: 15 interactions with chain N, 4 interactions with chain Q Hydrophobic interactions: N:K.41, N:V.44, N:L.47, N:W.51, N:W.51, N:W.51, N:K.74, N:V.75, N:F.79, N:F.79, N:F.118, Q:L.114 Hydrogen bonds: N:K.41, N:N.82, N:V.85, Q:D.112, Q:S.113, Q:S.113 Salt bridges: N:K.41

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.18: 12 residues within 4Å: Chain O: S.4, A.5, T.6, L.8, I.9 Chain P: L.3, V.6, L.7, R.9, G.10, Q.13, Y.23 11 PLIP interactions: 7 interactions with chain P, 3 interactions with chain O, 1 interactions with chain G Hydrophobic interactions: P:L.3, P:L.7, O:L.8, O:I.9 Water bridges: P:Q.13, P:Q.13, P:Q.13, P:Q.13, G:E.85 Salt bridges: P:R.9 Hydrogen bonds: O:T.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kampjut, D. et al., The coupling mechanism of mammalian respiratory complex I. Science (2020)

Release Date

2020-10-07

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
Mitochondrial complex I, 24 kDa subunit: B
NADH:ubiquinone oxidoreductase core subunit S1: C
Mitochondrial complex I, 49 kDa subunit: D
NADH:ubiquinone oxidoreductase core subunit S3: E
Mitochondrial complex I, PSST subunit: F
Mitochondrial complex I, TYKY subunit: G
Mitochondrial complex I, 10 kDa subunit: H
Mitochondrial complex I, 13 kDa subunit: I
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: J
NADH:ubiquinone oxidoreductase subunit A9: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: L
Mitochondrial complex I, B13 subunit: M
NADH:ubiquinone oxidoreductase subunit A6: N
Mitochondrial complex I, B14.5a subunit: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: P
Acyl carrier protein: Q
Mitochondrial complex I, B16.6 subunit: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
a

I
b

J
c

K
d

L
e

M
f

N
g

O
h

P
i

Q
j

R
q

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

Mitochondrial complex I, 24 kDa subunit

NADH:ubiquinone oxidoreductase core subunit S1

Mitochondrial complex I, 49 kDa subunit

NADH:ubiquinone oxidoreductase core subunit S3

Mitochondrial complex I, PSST subunit

Mitochondrial complex I, TYKY subunit

Mitochondrial complex I, 10 kDa subunit

Mitochondrial complex I, 13 kDa subunit

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Mitochondrial complex I, B13 subunit

NADH:ubiquinone oxidoreductase subunit A6

Mitochondrial complex I, B14.5a subunit

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

Acyl carrier protein

Mitochondrial complex I, B16.6 subunit

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