SMTL ID : 8ueq.1

In-situ complex I with Q10 (State-beta)

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 SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 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 SF4.6: 13 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, 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 SF4.7: 12 residues within 4Å: Chain D: I.392 Chain G: H.124, D.127, C.128, C.131, Q.133, G.134, C.137, Q.140, R.175, 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 SF4.8: 12 residues within 4Å: Chain G: M.173, C.176, I.177, Q.178, C.179, T.180, C.182, V.206, 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 SF4.11: 12 residues within 4Å: Chain I: H.128, C.150, P.151, I.155, I.174, C.179, I.180, Y.181, C.182, G.183, C.185, E.196 6 PLIP interactions: 6 interactions with chain I, Salt bridges: I:E.196 Metal complexes: I:H.128, I:C.150, I:C.179, I:C.182, I:C.185 SF4.12: 13 residues within 4Å: Chain I: C.140, I.141, A.142, C.143, K.144, L.145, C.146, Y.172, C.189, P.190, 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

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

PC1.2: 13 residues within 4Å: Chain A: L.24, Q.26, N.28 Chain B: L.112, V.116, R.120, R.251, L.252, W.255, R.258 Chain P: D.90, E.311 Ligands: PC1.24 6 PLIP interactions: 1 interactions with chain A, 2 interactions with chain P, 3 interactions with chain B Hydrophobic interactions: A:L.24, B:R.251, B:L.252 Salt bridges: P:D.90, P:E.311, B:R.258 PC1.22: 15 residues within 4Å: Chain 3: R.11, V.12, P.13, L.14, Q.15, F.16, R.81 Chain 4: F.3, F.4 Chain N: L.206, V.336, M.339, A.342, L.346, N.347 9 PLIP interactions: 6 interactions with chain N, 3 interactions with chain 3 Hydrophobic interactions: N:L.206, N:V.336, N:V.336, N:M.339, N:A.342, N:L.346, 3:R.11 Hydrogen bonds: 3:L.14 Salt bridges: 3:R.81 PC1.24: 16 residues within 4Å: Chain B: L.115, W.118 Chain H: F.19, V.39, G.41, P.42, L.45, L.46, L.53 Chain I: F.115 Ligands: PC1.2 Chain g: F.28, R.29, N.31, W.75, D.76 15 PLIP interactions: 7 interactions with chain H, 5 interactions with chain B, 3 interactions with chain g Hydrophobic interactions: H:F.19, H:P.42, H:L.45, H:L.46, H:L.46, H:L.46, H:L.53, B:L.115, B:L.115, B:W.118, B:W.118, B:W.118, g:F.28 Hydrogen bonds: g:N.31 Salt bridges: g:D.76

1 x U10: UBIQUINONE-10(Non-covalent)

U10.3: 31 residues within 4Å: Chain B: W.125, M.139, D.149, V.154, F.155, R.156 Chain D: P.102, A.103, A.104, H.105, T.202, L.205, D.206, F.214 Chain H: I.11, L.14, L.15, A.18, E.24, P.48, I.49, D.51, A.52, L.55, E.202, N.212, F.220, F.224, M.225, Y.228, R.274 18 PLIP interactions: 3 interactions with chain D, 10 interactions with chain H, 5 interactions with chain B Hydrophobic interactions: D:L.205, D:F.214, H:I.11, H:L.14, H:L.15, H:A.18, H:I.49, H:A.52, H:E.202, H:F.220, H:F.224, H:F.224, B:W.125, B:F.155, B:F.155, B:F.155, B:R.156 Hydrogen bonds: D:H.105

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

FES.4: 10 residues within 4Å: Chain E: C.135, T.137, P.139, C.140, C.176, L.177, G.178, 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: 8 residues within 4Å: Chain G: 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.5: 18 residues within 4Å: Chain F: G.87, R.88, G.89, A.91, K.98, N.116, D.118, E.119, Y.204, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:Y.204, F:E.208, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:R.88, F:G.89, F:D.118, F:E.119, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247 Salt bridges: F:K.98

1 x K: POTASSIUM ION(Non-covalent)

K.10: 5 residues within 4Å: Chain G: Q.133, I.223, C.226, V.228, L.231 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:I.223, G:C.226

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.13: 10 residues within 4Å: Chain L: N.400, P.483, Y.485, M.486, T.489, I.492 Chain b: Y.153, Q.154, P.155 Chain e: H.4 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain b Hydrophobic interactions: L:Y.485, b:Q.154

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

3PE.14: 14 residues within 4Å: Chain 3: V.56 Chain M: T.90, R.91, L.94, M.98, I.131, R.135 Chain N: P.238, V.239, S.242, L.243, M.245, V.246 Chain O: Q.331 8 PLIP interactions: 3 interactions with chain M, 3 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: M:L.94, M:I.131, N:P.238, N:L.243, N:V.246 Salt bridges: M:R.91, O:K.340 Hydrogen bonds: O:Q.331

2 x CDL: CARDIOLIPIN(Covalent)

CDL.15: 19 residues within 4Å: Chain N: P.3, Y.6, T.7, I.10, Q.125, L.128, T.132, W.133, I.209, L.213, M.217, K.321, M.323, K.324, L.325 Chain O: P.42, L.43, H.294, R.295 14 PLIP interactions: 12 interactions with chain N, 2 interactions with chain O Hydrophobic interactions: N:Y.6, N:T.7, N:I.10, N:I.10, N:I.10, N:L.128, N:W.133, N:I.209, N:L.325 Hydrogen bonds: N:Q.125, N:K.324 Salt bridges: N:K.321, O:H.294, O:R.295 CDL.21: 16 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, Q.13, V.33 Chain h: A.5, T.6, I.9 16 PLIP interactions: 3 interactions with chain h, 6 interactions with chain g, 6 interactions with chain 0, 1 interactions with chain H Hydrophobic interactions: h:I.9, g:L.3, g:L.7, 0:W.2, 0:L.6, 0:P.7, 0:A.10, H:Y.43 Hydrogen bonds: h:T.6, h:T.6, g:Q.13, 0:M.1, 0:M.1 Salt bridges: g:R.9, g:R.9, g:R.9

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.16: 20 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, L.133, Q.134, L.137, R.141, R.163, D.168, F.171, M.175, K.223 Ligands: MG.17 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: 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:Q.134 Salt bridges: O:K.72, O:K.72, O:R.163, O:K.223 pi-Stacking: O:F.171, O:F.171

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 2 residues within 4Å: Chain O: C.69 Ligands: GTP.16 No protein-ligand interaction detected (PLIP)

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

NDP.18: 26 residues within 4Å: Chain B: R.258 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, F.139, V.144, F.145, I.167, H.169, Y.180, K.184, P.203, S.204, D.205, I.206, R.212 26 PLIP interactions: 25 interactions with chain P, 1 interactions with chain B Hydrophobic interactions: P:I.206 Hydrogen bonds: P:T.62, P:T.62, P:T.62, P:G.63, P:L.65, P:R.85, P:R.85, P:C.86, P:V.130, P:G.131, P:R.132, P:Y.180, P:K.184, P:D.205, P:I.206, P:I.206, P:R.212, B:R.258 Salt bridges: P:R.85, P:R.132, P:R.132, P:R.212, P:R.212 pi-Stacking: P:H.169 pi-Cation interactions: P:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.19: 5 residues within 4Å: Chain R: C.86, G.88, H.95, C.111, C.114 4 PLIP interactions: 4 interactions with chain R Metal complexes: 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.20: 16 residues within 4Å: Chain T: S.112, L.113 Chain W: K.29, V.32, R.33, L.35, W.39, G.59, K.62, V.63, M.66, F.67, N.70, A.71, V.73, F.106 15 PLIP interactions: 13 interactions with chain W, 2 interactions with chain T Hydrophobic interactions: W:K.29, W:V.32, W:W.39, W:W.39, W:K.62, W:M.66, W:F.67, W:V.73, W:F.106, W:F.106, T:L.113 Hydrogen bonds: W:N.70, W:N.70, T:S.112 Salt bridges: W:R.33 EHZ.23: 16 residues within 4Å: Chain U: D.111, S.112, L.113 Chain d: H.12, Q.13, V.16, A.23, L.27, R.47, F.48, H.51, K.52, A.60, L.63, A.67, E.70 13 PLIP interactions: 10 interactions with chain d, 3 interactions with chain U Hydrophobic interactions: d:Q.13, d:A.23, d:L.27, d:L.27, d:F.48, d:A.67, U:L.113 Hydrogen bonds: d:Q.13, d:R.47, d:R.47, d:K.52, U:D.111, U:L.113

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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