SMTL ID : 8uew.1

In-situ complex I, Deactive class05

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

3PE.1: 15 residues within 4Å: Chain 1: A.12, E.16, L.19, S.22, F.23, A.24, G.26, G.27 Chain A: I.96, A.99, A.103, W.106 Chain H: K.291, P.295, M.302 9 PLIP interactions: 2 interactions with chain H, 5 interactions with chain A, 2 interactions with chain 1 Hydrophobic interactions: H:P.295, A:I.96, A:A.99, A:A.103, A:W.106, A:W.106, 1:F.23, 1:F.23 Salt bridges: H:K.291 3PE.15: 19 residues within 4Å: Chain L: T.166, Q.170, L.173, Y.174, I.177, G.228, L.229, Y.529, P.530, M.533, H.534, T.538, N.541, L.542 Chain M: M.401, L.405 Chain b: N.115, R.116, V.117 12 PLIP interactions: 10 interactions with chain L, 1 interactions with chain b, 1 interactions with chain M Hydrophobic interactions: L:Q.170, L:L.173, L:Y.174, L:Y.174, L:I.177, L:L.229, L:L.542, b:R.116, M:L.405 Hydrogen bonds: L:Q.170 Salt bridges: L:H.534, L:H.534 3PE.17: 13 residues within 4Å: Chain L: L.286, L.290, I.293, T.294, I.414, S.417, R.425, A.501, L.504, T.508, Y.520, S.523 Chain d: W.30 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain d Hydrophobic interactions: L:L.286, L:L.290, L:T.294, L:I.414 Hydrogen bonds: L:Y.520, d:W.30 Salt bridges: L:R.425 3PE.19: 17 residues within 4Å: Chain 3: V.56 Chain M: P.13, W.16, T.90, L.94, M.98, L.101, V.127, I.131, R.135 Chain N: P.238, V.239, S.242, M.245, V.246 Chain O: K.340, Y.341 12 PLIP interactions: 2 interactions with chain N, 2 interactions with chain O, 7 interactions with chain M, 1 interactions with chain 3 Hydrophobic interactions: N:P.238, N:V.246, M:W.16, M:W.16, M:L.94, M:L.94, M:L.101, M:V.127, M:I.131, 3:V.56 Hydrogen bonds: O:Y.341 Salt bridges: O:K.340 3PE.26: 13 residues within 4Å: Chain L: M.576, V.577, Q.580 Chain N: P.110, F.113, L.160 Chain Y: V.36, Y.39, S.40, L.43, K.44, Y.59 Ligands: 3PE.27 11 PLIP interactions: 7 interactions with chain Y, 1 interactions with chain L, 3 interactions with chain N Hydrophobic interactions: Y:Y.39, Y:Y.39, Y:L.43, L:V.577, N:P.110, N:F.113, N:L.160 Hydrogen bonds: Y:Y.59 Salt bridges: Y:K.44, Y:K.44, Y:K.44 3PE.27: 12 residues within 4Å: Chain Y: L.6, Y.9, S.25, I.28, G.29, V.36, Y.59, T.62, S.63, G.67, F.70 Ligands: 3PE.26 7 PLIP interactions: 7 interactions with chain Y Hydrophobic interactions: Y:L.6, Y:Y.9, Y:Y.9, Y:Y.9, Y:V.36, Y:F.70, Y:F.70

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

SF4.2: 13 residues within 4Å: Chain B: A.132, C.133, C.134, G.169, T.170, G.196, S.197, C.198, G.227, C.228, P.229 Chain D: R.151, H.236 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.133, B:C.134, B:C.198, B:C.228 SF4.5: 13 residues within 4Å: Chain F: I.205, P.223, C.379, G.380, Q.381, C.382, C.385, R.386, T.423, I.424, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.6: 11 residues within 4Å: Chain G: H.124, D.127, C.128, C.131, Q.133, G.134, C.137, L.139, Q.140, V.228, G.229 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.127 Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.7: 13 residues within 4Å: Chain G: C.176, I.177, Q.178, C.179, T.180, R.181, C.182, V.206, I.225, C.226, V.228, A.230, L.231 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.10: 13 residues within 4Å: Chain I: H.128, C.150, P.151, A.152, A.154, I.155, C.179, I.180, Y.181, C.182, G.183, F.184, C.185 7 PLIP interactions: 7 interactions with chain I, Metal complexes: I:C.150, I:C.150, I:C.179, I:C.179, I:C.182, I:C.182, I:C.185 SF4.11: 13 residues within 4Å: Chain I: C.140, I.141, A.142, C.143, K.144, L.145, C.146, I.157, Y.172, C.189, V.191, A.193, I.194 5 PLIP interactions: 5 interactions with chain I, Metal complexes: I:C.140, I:C.143, I:C.146, I:Y.172, I:C.189

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

FES.3: 10 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, R.143, C.176, L.177, A.179, C.180, M.185 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.135, E:C.140, E:C.176, E:C.180 FES.9: 10 residues within 4Å: Chain G: R.62, F.63, C.64, Y.65, G.73, N.74, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 18 residues within 4Å: Chain F: G.87, G.89, A.91, K.98, N.116, D.118, E.119, G.120, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.204, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:N.116, F:N.116, F:E.119, F:G.120, F:E.209, F:E.209, F:N.244, F:N.244, F:T.247, F:T.247 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:I.223, G:C.226, G:V.228

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

PC1.12: 24 residues within 4Å: Chain 1: V.18, I.25 Chain D: R.279 Chain H: W.179, P.180, A.182, M.183, F.186, I.187, F.198, Y.277, H.287, L.288, S.292, F.293, L.296, W.303 Chain I: T.87, L.88, L.89, W.90, L.93, L.97 Chain Z: L.43 24 PLIP interactions: 11 interactions with chain H, 9 interactions with chain I, 2 interactions with chain D, 1 interactions with chain Z, 1 interactions with chain 1 Hydrophobic interactions: H:W.179, H:P.180, H:M.183, H:F.186, H:F.186, H:I.187, H:I.187, H:F.198, H:Y.277, H:L.296, H:W.303, I:L.88, I:L.89, I:W.90, I:W.90, I:W.90, I:W.90, I:W.90, I:L.93, I:L.97, Z:L.43, 1:I.25 Salt bridges: D:R.279, D:R.279 PC1.13: 19 residues within 4Å: Chain H: M.183, W.272 Chain I: D.82, A.85, Q.86, T.91, V.94, R.95, G.98, L.101 Chain Z: R.27, R.28, G.29, L.30, S.31, G.32, M.35 Chain h: W.15, A.16 9 PLIP interactions: 1 interactions with chain H, 5 interactions with chain I, 2 interactions with chain Z, 1 interactions with chain h Hydrophobic interactions: H:W.272, I:T.91, I:L.101, h:W.15 Salt bridges: I:D.82, I:R.95, I:R.95, Z:R.27, Z:R.28 PC1.14: 8 residues within 4Å: Chain 4: L.14 Chain A: N.83, T.86, T.89 Chain J: S.148, Y.149, T.151, W.152 6 PLIP interactions: 3 interactions with chain J, 1 interactions with chain 4, 2 interactions with chain A Hydrophobic interactions: J:W.152, J:W.152, 4:L.14, A:T.89 Hydrogen bonds: J:T.151, A:N.83 PC1.16: 16 residues within 4Å: Chain 6: L.99, S.103, V.106, A.107, Y.108 Chain 8: H.89 Chain L: W.66 Chain M: V.67, L.68, W.71, I.317, P.443, L.446, L.447, L.449, N.450 15 PLIP interactions: 11 interactions with chain M, 3 interactions with chain 6, 1 interactions with chain 8 Hydrophobic interactions: M:V.67, M:L.68, M:W.71, M:W.71, M:I.317, M:P.443, M:L.446, M:L.446, M:L.447, M:L.449, M:N.450, 6:L.99, 6:V.106, 6:A.107 Salt bridges: 8:K.93 PC1.28: 14 residues within 4Å: Chain 5: F.98, C.102, R.106 Chain 6: L.101, T.104, F.105 Chain 7: I.117, W.120, T.124, F.125, D.127 Chain M: L.36, I.37, S.40 9 PLIP interactions: 4 interactions with chain M, 4 interactions with chain 7, 1 interactions with chain 5 Hydrophobic interactions: M:L.36, M:I.37, 7:I.117, 7:W.120, 7:F.125 Hydrogen bonds: M:S.40 Salt bridges: M:K.3, 7:D.127, 5:R.106

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.18: 19 residues within 4Å: Chain M: P.159, V.162, A.163, Y.166, S.191, F.194, M.195, L.197, A.198, M.201 Chain N: E.274, I.276, I.277, T.280, L.281, M.284 Chain Y: E.131, G.132, W.133 15 PLIP interactions: 4 interactions with chain N, 2 interactions with chain Y, 9 interactions with chain M Hydrophobic interactions: N:I.276, N:I.277, N:T.280, Y:W.133, Y:W.133, M:P.159, M:V.162, M:F.194, M:F.194, M:L.197, M:A.198, M:M.201 Hydrogen bonds: N:E.274, M:S.191, M:S.191

2 x CDL: CARDIOLIPIN(Covalent)

CDL.20: 19 residues within 4Å: Chain N: P.3, I.4, Y.6, T.7, M.11, K.46, Q.125, L.128, L.129, T.132, W.133, L.136, L.206, L.213, M.217, K.321, L.325 Chain O: P.42, V.46 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.4, N:W.133, N:W.133, N:L.136, N:L.213, O:V.46 Hydrogen bonds: N:T.7 Salt bridges: N:K.46 CDL.31: 18 residues within 4Å: Chain 0: M.1, W.2, F.3, L.6, P.7, A.10 Chain H: Y.43 Chain g: L.3, V.6, L.7, R.9, Y.23, V.33 Chain h: S.4, A.5, T.6, V.8, I.9 15 PLIP interactions: 3 interactions with chain 0, 4 interactions with chain h, 6 interactions with chain g, 2 interactions with chain H Hydrophobic interactions: 0:W.2, 0:L.6, 0:A.10, h:V.8, h:I.9, g:L.3, g:L.7, g:V.33, H:Y.43, H:Y.43 Hydrogen bonds: h:T.6, h:T.6, g:R.9, g:R.9 Salt bridges: g:R.9

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.21: 18 residues within 4Å: Chain O: N.67, I.68, C.69, S.70, G.71, K.72, G.73, E.90, L.116, Y.120, Q.134, L.137, R.141, R.163, D.168, F.171, M.175 Ligands: MG.22 18 PLIP interactions: 18 interactions with chain O Hydrogen bonds: O:N.67, O:C.69, O:S.70, O:G.71, O:K.72, O:G.73, O:Y.120, O:Q.134, O:Q.134, O:R.141, O:R.141, O:R.163, O:D.168 Salt bridges: O:K.72, O:K.72, O:D.168 pi-Stacking: O:F.171, O:F.171

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.22: 1 residues within 4Å: Ligands: GTP.21 No protein-ligand interaction detected (PLIP)

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

NDP.23: 22 residues within 4Å: Chain P: 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, E.133, F.139, F.145, I.167, K.184, P.203, D.205, I.206, R.212 24 PLIP interactions: 24 interactions with chain P Hydrophobic interactions: P:P.203, P:I.206 Hydrogen bonds: P:G.60, P:T.62, P:T.62, P:T.62, P:F.64, P:L.65, P:R.85, P:V.130, P:G.131, P:E.133, P:K.184, P:I.206, P:I.206, P:R.212 Salt bridges: P:R.85, P:R.132, P:R.132, P:R.212, P:R.212 pi-Cation interactions: P:R.85, P:R.85, P:H.169

1 x ZN: ZINC ION(Non-covalent)

ZN.24: 4 residues within 4Å: Chain R: C.86, H.95, C.111, C.114 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:C.86, R:C.86, R:H.95, R:C.111, R:C.114

2 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate(Non-covalent)

EHZ.25: 18 residues within 4Å: Chain T: D.111, S.112, L.113 Chain W: K.29, V.32, L.35, W.39, M.66, F.67, N.70, A.71, H.72, V.73, V.79, L.82, V.83, G.86, F.106 17 PLIP interactions: 14 interactions with chain W, 3 interactions with chain T Hydrophobic interactions: W:W.39, W:W.39, W:W.39, W:W.39, W:F.67, W:F.67, W:A.71, W:V.73, W:L.82, W:F.106 Hydrogen bonds: W:N.70, W:N.70, W:A.71, W:A.71, T:S.112, T:S.112, T:L.113 EHZ.30: 15 residues within 4Å: Chain U: D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, M.44, R.47, F.48, H.51, K.52, A.60, L.63, L.64, A.67 6 PLIP interactions: 6 interactions with chain d Hydrophobic interactions: d:Q.13, d:F.48, d:L.63, d:A.67 Hydrogen bonds: d:R.47, d:K.52

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.29: 9 residues within 4Å: Chain L: N.400, L.409, Y.485, T.489 Chain b: S.152, Y.153, Q.154 Chain e: G.2, L.5 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain b Hydrophobic interactions: L:L.409, L:Y.485 Hydrogen bonds: b:Y.153, b:Q.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, W. et al., High-resolution in situ structures of mammalian respiratory supercomplexes. Nature (2024)

Release Date

2024-06-19

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: I
NADH-ubiquinone oxidoreductase chain 6: J
NADH-ubiquinone oxidoreductase chain 4L: K
NADH-ubiquinone oxidoreductase chain 5: L
NADH-ubiquinone oxidoreductase chain 4: M
NADH-ubiquinone oxidoreductase chain 2: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: O
NADH:ubiquinone oxidoreductase subunit A9: P
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: Q
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: S
NADH:ubiquinone oxidoreductase subunit AB1: TU
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1: V
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: W
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: Y
NADH:ubiquinone oxidoreductase subunit A13: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: 1
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial: 2
NADH dehydrogenase [ubiquinone] 1 subunit C2: 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus scrofa]: 5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial: 7
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: 8
NADH:ubiquinone oxidoreductase subunit B2: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3: a
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: b
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: c
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: f
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: g
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: h
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1A

B
1B

C
1C

D
1D

E
1E

F
1F

G
1G

H
1H

I
1I

J
1J

K
1K

L
1L

M
1M

N
1N

O
1O

P
1P

Q
1Q

R
1R

S
1S

T
1T

U
1U

V
1V

W
1W

X
1X

Y
1Y

Z
1Z

0
1a

1
1b

2
1c

3
1d

4
1e

5
1f

6
1g

7
1h

8
1i

9
1j

a
1k

b
1l

c
1m

d
1n

e
1o

f
1p

g
1q

h
1r

i
1s

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH:ubiquinone oxidoreductase subunit A9

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

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH:ubiquinone oxidoreductase subunit AB1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH:ubiquinone oxidoreductase subunit A13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus scrofa]

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH:ubiquinone oxidoreductase subunit B2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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