SMTL ID : 7zkp.1

Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 21 residues within 4Å: Chain E: H.27, S.129, S.130, L.131, P.154, W.155, F.156, F.158, V.159, N.160 Chain F: Y.332 Chain H: N.85, Y.86, F.88, T.89, I.90, L.93 Chain I: F.160, L.163 Chain J: L.41, R.48 25 PLIP interactions: 6 interactions with chain H, 3 interactions with chain J, 1 interactions with chain F, 12 interactions with chain E, 3 interactions with chain I Hydrophobic interactions: H:Y.86, H:Y.86, H:F.88, H:T.89, H:I.90, H:L.93, J:L.41, J:L.41, F:Y.332, E:W.155, E:W.155, E:W.155, E:F.158, E:F.158, I:F.160, I:L.163, I:L.163 Hydrogen bonds: J:R.48, E:S.129, E:S.130, E:L.131, E:F.158, E:N.160, E:N.160 Salt bridges: E:H.27 CDL.4: 19 residues within 4Å: Chain E: F.28, T.47, K.73, V.77, M.80, F.83, A.84, F.87 Chain G: L.4, S.8, T.11, F.12, M.15 Chain H: L.96 Chain J: F.8, W.9, Y.15, I.34 Ligands: 3PE.5 15 PLIP interactions: 10 interactions with chain E, 1 interactions with chain H, 3 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: E:F.28, E:T.47, E:M.80, E:F.83, E:F.83, E:F.83, E:A.84, E:F.87, E:F.87, H:L.96, J:I.34, G:L.4 Salt bridges: E:K.73 Hydrogen bonds: J:F.8, J:Y.15

1 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.2: 11 residues within 4Å: Chain D: F.45, Y.46, L.49 Chain F: I.326, T.330, I.333, F.334 Chain J: A.39, L.43, L.51, Y.52 13 PLIP interactions: 5 interactions with chain D, 3 interactions with chain J, 5 interactions with chain F Hydrophobic interactions: D:F.45, D:F.45, D:F.45, D:Y.46, D:L.49, J:A.39, J:L.43, J:L.51, F:I.326, F:I.333, F:F.334, F:F.334, F:F.334

1 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.3: 22 residues within 4Å: Chain G: L.36, V.37, S.40, Y.43, Y.67, M.70, F.74, L.310, Y.311, T.314, L.449, G.453, Y.456, I.460, I.463, F.464, Y.467 Chain K: W.43, L.46, G.47, V.53 Ligands: T7X.6 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain K Hydrophobic interactions: G:F.74, G:Y.311, G:L.449, G:Y.456, G:Y.456, G:I.460, K:W.43, K:L.46 pi-Cation interactions: G:Y.43

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

3PE.5: 21 residues within 4Å: Chain F: P.318, L.325 Chain H: I.99, F.102, V.103, I.106, N.107 Chain J: N.5, Y.15, L.16, W.18, S.19, R.23, L.26, F.27, A.29, F.30, A.31, G.33, I.34 Ligands: CDL.4 20 PLIP interactions: 14 interactions with chain J, 4 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: J:L.16, J:L.26, J:L.26, J:F.27, J:A.29, J:F.30, J:F.30, J:F.30, J:F.30, J:F.30, J:F.30, H:I.99, H:I.99, H:F.102, H:I.106, F:P.318, F:L.325 Hydrogen bonds: J:N.5, J:Y.15 Salt bridges: J:R.23

1 x T7X: Phosphatidylinositol(Non-covalent)

T7X.6: 19 residues within 4Å: Chain E: W.59, L.60 Chain G: F.74, S.437, V.438, Y.441, L.449 Chain K: K.18, R.25, K.27, Y.31, Y.32, G.35, F.38, S.39, A.42, W.43, L.46 Ligands: CPL.3 14 PLIP interactions: 8 interactions with chain K, 5 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: K:A.42, K:W.43, K:L.46, G:F.74, G:Y.441, G:Y.441, G:Y.441, G:L.449 Hydrogen bonds: K:R.25, K:R.25, K:S.39, E:W.59 Salt bridges: K:K.18, K:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiller, J. et al., Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling. Sci Adv (2022)

Release Date

2022-11-23

Peptides

Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I): A
NADH-ubiquinone oxidoreductase chain 4L: B
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I): C
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I): D
NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein: E
NADH-ubiquinone oxidoreductase chain 1: F
NADH dehydrogenase subunit 2: G
NADH-ubiquinone oxidoreductase chain 3: H
NADH-ubiquinone oxidoreductase chain 6: I
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I): J
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I): K
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I): L
assembly factor CIA84: M
CIA30 domain-containing protein: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
L

C
U

D
W

E
X

F
1

G
2

H
3

I
6

J
g

K
b

L
9

M
C

N
A

Membrane

We predict this structure to be a membrane protein.
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Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

NADH-ubiquinone oxidoreductase chain 4L

Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase subunit 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 6

subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

assembly factor CIA84

CIA30 domain-containing protein

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