SMTL ID : 7zme.1

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 2) - membrane arm

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

3PE.1: 13 residues within 4Å: Chain A: P.189, I.192, I.196, V.199, F.207, T.330, I.337, F.345, V.349, L.350, I.353 Chain W: F.28, I.32 Ligand excluded by PLIP 3PE.2: 11 residues within 4Å: Chain A: F.88, L.91, N.105, Y.113 Chain C: S.2, M.4, S.5, I.8 Chain F: F.59, I.62, N.67 Ligand excluded by PLIP 3PE.9: 13 residues within 4Å: Chain B: F.422, P.426, L.427, L.430 Chain D: S.19, N.151, K.153, S.154, I.157, I.158, L.161, P.187, P.188 Ligand excluded by PLIP 3PE.10: 9 residues within 4Å: Chain D: I.506, I.509, Y.510 Chain E: I.61, F.62, R.63 Chain Z: Y.69 Ligands: 3PE.30, PC1.31 Ligand excluded by PLIP 3PE.13: 2 residues within 4Å: Chain D: Y.74, K.77 Ligand excluded by PLIP 3PE.15: 14 residues within 4Å: Chain B: P.259, L.321, I.325 Chain E: L.623, Y.634, V.637, L.641, Y.645, L.655, L.662, M.666 Chain J: F.34, R.38, R.43 Ligand excluded by PLIP 3PE.16: 15 residues within 4Å: Chain B: I.324, I.469, I.476 Chain E: L.603, F.604, G.605, G.608, L.609, R.611, G.612, L.613, I.660 Chain J: R.108, V.119 Ligands: 3PE.22 Ligand excluded by PLIP 3PE.17: 20 residues within 4Å: Chain E: L.290, F.294, Q.296, F.420, L.423, K.427, L.431, F.536, A.540, L.543, S.544, V.551, K.555, I.563, F.564 Chain M: V.23, H.24 Chain R: F.127, S.130, F.131 Ligand excluded by PLIP 3PE.19: 9 residues within 4Å: Chain E: R.558, F.559, N.562, I.563, F.566, F.567 Chain M: K.64 Chain R: Q.123, F.127 Ligand excluded by PLIP 3PE.20: 5 residues within 4Å: Chain E: F.48, F.52 Chain G: Y.45, L.47 Chain X: F.64 Ligand excluded by PLIP 3PE.22: 10 residues within 4Å: Chain E: F.604, R.611 Chain J: P.107, R.108, G.111, F.112, A.114, L.115 Chain Y: W.31 Ligands: 3PE.16 Ligand excluded by PLIP 3PE.25: 9 residues within 4Å: Chain A: I.192 Chain P: R.23, G.24, L.25, R.27, P.30, L.31, G.34, A.35 Ligand excluded by PLIP 3PE.28: 16 residues within 4Å: Chain A: P.186, P.189, L.357, L.360, V.361, I.364, F.368 Chain P: M.39, W.43, Y.44, V.47, K.48, R.51 Chain W: R.47, I.50, D.52 Ligand excluded by PLIP 3PE.29: 19 residues within 4Å: Chain A: P.352, A.356 Chain B: V.15 Chain C: T.99, V.103, L.106, G.107 Chain W: T.5, Y.15, W.18, A.19, R.23, L.26, F.27, S.29, V.30, G.33, A.34 Ligands: CDL.27 Ligand excluded by PLIP 3PE.30: 10 residues within 4Å: Chain E: I.61 Chain X: V.37, Y.48, H.52 Chain Z: I.62, S.65, F.66, Y.69, N.70 Ligands: 3PE.10 Ligand excluded by PLIP 3PE.32: 12 residues within 4Å: Chain D: I.88, L.91, I.92, I.95 Chain N: Y.95, G.96, S.100, V.103, F.104, A.107 Chain Z: I.90, Y.93 Ligand excluded by PLIP

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

PC1.3: 7 residues within 4Å: Chain A: Y.26, N.45, A.46, G.48, I.49, L.52, L.53 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.26, A:L.52, A:L.53, A:L.53 Hydrogen bonds: A:A.46, A:G.48, A:I.49 PC1.6: 9 residues within 4Å: Chain B: A.34, I.37, L.38, T.41, I.73 Chain Q: H.43, Y.89 Chain S: W.49 Ligands: LMN.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.34, B:I.37, B:I.37, B:I.73 PC1.7: 7 residues within 4Å: Chain A: L.60, L.64 Chain C: L.23, I.24, F.25, A.26, P.27 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.60, A:L.64, A:L.64, C:F.25, C:F.25 PC1.12: 19 residues within 4Å: Chain B: L.331, V.475, I.476, V.479, N.483, K.486, Y.491 Chain D: V.202, R.203, F.206, Y.207, L.210, Y.211, L.214 Chain E: P.606, L.609, E.610, L.613, V.614 17 PLIP interactions: 4 interactions with chain E, 6 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: E:P.606, E:L.609, E:L.613, E:V.614, B:L.331, B:V.475, B:I.476, B:V.479, B:V.479, D:F.206, D:L.210, D:Y.211, D:Y.211, D:Y.211 Hydrogen bonds: B:N.483, D:R.203 Salt bridges: D:R.203 PC1.14: 30 residues within 4Å: Chain D: T.407, Q.408, P.411, S.414, L.415, F.418, L.422, T.427, P.428, L.429, Y.469, F.474 Chain E: S.13, V.14, G.17, F.18, H.109, R.112, Y.116, L.119, M.123, V.138, E.141, G.142, V.145, L.149 Chain X: S.15, A.17, G.19, W.20 26 PLIP interactions: 7 interactions with chain D, 16 interactions with chain E, 3 interactions with chain X Hydrophobic interactions: D:T.407, D:L.415, D:L.422, D:T.427, D:P.428, D:L.429, D:F.474, E:V.14, E:F.18, E:F.18, E:L.119, E:L.119, E:E.141, E:V.145, E:L.149, E:L.149 Hydrogen bonds: E:Y.116, X:S.15, X:G.19, X:G.19 Water bridges: E:Q.111, E:R.112, E:R.112 Salt bridges: E:H.109, E:R.112, E:R.112 PC1.18: 19 residues within 4Å: Chain D: L.334, F.460, Y.467 Chain E: Q.162, I.165, S.166, L.169, T.170, L.229, M.235, Y.577, N.578, T.582, I.585, L.586 Chain R: S.108, P.109, Y.110, Y.112 13 PLIP interactions: 6 interactions with chain E, 5 interactions with chain D, 2 interactions with chain R Hydrophobic interactions: E:I.165, E:L.169, E:L.229, E:I.585, E:L.586, D:L.334, D:L.334, D:F.460, D:Y.467, D:Y.467 Hydrogen bonds: E:N.578, R:Y.110, R:Y.112 PC1.31: 22 residues within 4Å: Chain D: L.132, I.135, L.374, F.378, F.503, L.507, F.513, V.514 Chain N: W.98, L.101, A.105, Y.108, A.109, K.111, D.113 Chain Z: S.65, I.68, Y.69, S.72, R.73 Ligands: CDL.8, 3PE.10 18 PLIP interactions: 11 interactions with chain D, 4 interactions with chain N, 3 interactions with chain Z Hydrophobic interactions: D:L.132, D:I.135, D:L.374, D:F.378, D:F.503, D:F.503, D:L.507, D:F.513, D:F.513, D:F.513, D:V.514, N:L.101, N:L.101, N:A.105, Z:I.68 Salt bridges: N:D.113, Z:R.73 Hydrogen bonds: Z:S.72

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 30 residues within 4Å: Chain B: I.73, L.77, Q.80, F.84, K.88, F.101, I.375, S.533, S.534, P.535, I.538, T.539, I.542, I.543 Chain Q: L.57, M.58, I.61, S.62 Chain S: W.8, F.11, G.12, R.16, R.25, W.34, L.38, F.39, V.42, G.43, F.46 Ligands: LMN.5 27 PLIP interactions: 12 interactions with chain B, 3 interactions with chain Q, 12 interactions with chain S Hydrophobic interactions: B:I.73, B:L.77, B:I.375, B:I.538, B:I.538, B:I.542, B:I.542, B:I.543, Q:I.61, S:W.8, S:F.11, S:W.34, S:F.39, S:F.39, S:F.39, S:V.42, S:F.46, S:F.46, S:F.46 Hydrogen bonds: B:S.534, B:S.534, Q:S.62 Salt bridges: B:K.88, B:K.88, S:R.16, S:R.25 Water bridges: Q:I.61 CDL.8: 29 residues within 4Å: Chain D: L.412, L.415, I.419, K.491, F.494, F.495, F.498, S.502, I.506 Chain E: V.14, F.18 Chain N: L.75, W.76, F.94, Y.95, W.98, G.99, I.102, V.103 Chain X: W.14, P.16 Chain Z: G.52, A.53, A.54, I.57, A.58, G.61, S.64 Ligands: PC1.31 26 PLIP interactions: 10 interactions with chain D, 6 interactions with chain Z, 1 interactions with chain X, 4 interactions with chain N, 5 interactions with chain E Hydrophobic interactions: D:L.415, D:I.419, D:F.494, D:F.494, D:F.495, D:F.495, D:F.498, D:F.498, D:I.506, Z:A.54, Z:I.57, Z:I.57, Z:A.58, X:P.16, N:F.94, N:W.98, N:W.98, N:V.103, E:V.14, E:F.18, E:F.18, E:F.18 Salt bridges: D:K.491, E:K.22 Hydrogen bonds: Z:A.53, Z:A.54 CDL.21: 3 residues within 4Å: Chain I: P.2, V.3, L.8 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:V.3, I:V.3 Hydrogen bonds: I:V.3 CDL.26: 24 residues within 4Å: Chain A: Y.366 Chain B: M.3, L.7 Chain C: A.85, Y.86, A.89, L.92, I.93, G.96, I.97 Chain Q: H.28, E.128, S.129, R.130, L.131, P.154, W.155, F.156, F.158, V.159, N.160 Chain W: P.37, L.40, A.41 23 PLIP interactions: 5 interactions with chain C, 12 interactions with chain Q, 4 interactions with chain W, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:A.85, C:A.89, C:L.92, C:I.93, C:I.97, Q:W.155, Q:W.155, Q:F.156, Q:F.158, Q:F.158, W:P.37, W:L.40, W:L.40, W:A.41, A:Y.366, B:L.7 Hydrogen bonds: Q:H.28, Q:E.128, Q:R.130, Q:N.160 Salt bridges: Q:R.130, Q:R.130, Q:R.130 CDL.27: 17 residues within 4Å: Chain B: L.7, S.8, L.11, S.12, V.15 Chain C: G.96, T.99, I.100, V.103 Chain Q: K.73, R.76, F.80 Chain W: R.7, F.8, W.9, Y.15 Ligands: 3PE.29 15 PLIP interactions: 7 interactions with chain Q, 4 interactions with chain B, 3 interactions with chain W, 1 interactions with chain C Hydrophobic interactions: Q:F.80, Q:F.80, Q:F.80, B:L.7, B:L.11, B:V.15, W:F.8, W:W.9, C:I.100 Hydrogen bonds: Q:K.73, Q:K.73, W:F.8 Salt bridges: Q:K.73, Q:R.76 Water bridges: B:S.12

3 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.5: 25 residues within 4Å: Chain B: T.41, M.42, L.44, S.45, I.47, N.62, I.66, I.69, F.70, I.371, M.553, E.556, W.557, M.560, I.563, L.564, I.567 Chain Q: L.96 Chain S: W.8, L.50, I.53, Q.57, M.60 Ligands: CDL.4, PC1.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain S Hydrophobic interactions: B:I.66, B:I.69, B:F.70, B:I.371, B:W.557, B:M.560, S:W.8, S:L.50, S:I.53 Hydrogen bonds: B:L.44, B:L.44, B:M.560 LMN.11: 12 residues within 4Å: Chain B: L.468 Chain D: L.221, S.222, T.225, T.246, T.247, F.250, L.251, F.253, I.257 Chain J: Y.125, R.143 15 PLIP interactions: 9 interactions with chain D, 3 interactions with chain J, 3 interactions with chain B Hydrophobic interactions: D:L.221, D:F.250, D:L.251, D:F.253, D:I.257, B:L.468 Hydrogen bonds: D:T.246, D:T.247, D:T.247, J:Y.125, J:Y.125, J:R.143 Water bridges: D:S.228, B:L.459, B:D.460 LMN.23: 14 residues within 4Å: Chain D: L.444 Chain E: A.184, W.187, N.207, I.210, I.211 Chain J: K.184, Y.185, V.187 Chain Y: K.56, L.60, W.61, I.72, S.73 18 PLIP interactions: 5 interactions with chain Y, 8 interactions with chain E, 4 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: Y:W.61, Y:W.61, Y:I.72, Y:I.72, E:A.184, E:W.187, E:N.207, E:I.210, E:I.211, E:I.211, E:I.211, D:L.444 Hydrogen bonds: Y:W.61, E:N.207, J:K.184, J:K.184, J:Y.185, J:Y.185

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

ZMP.24: 24 residues within 4Å: Chain E: F.556 Chain L: S.98, L.99 Chain M: N.3, R.4, A.7, L.8, A.14, L.17, A.18, L.38, F.39, N.42, R.43, V.45, Q.51, L.54, L.55, T.58, L.62, W.65 Chain T: T.17, F.19, F.24 17 PLIP interactions: 12 interactions with chain M, 3 interactions with chain T, 2 interactions with chain E Hydrophobic interactions: M:R.4, M:A.14, M:L.17, M:F.39, M:R.43, M:V.45, M:Q.51, M:L.62, M:W.65, T:F.19, T:F.19, T:F.24, E:F.556, E:F.556 Hydrogen bonds: M:N.42, M:N.42 Salt bridges: M:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laube, E. et al., Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum. Sci Adv (2022)

Release Date

2022-11-30

Peptides

NADH-ubiquinone oxidoreductase chain 1: A
NADH dehydrogenase subunit 2: B
NADH-ubiquinone oxidoreductase chain 3: C
NADH-ubiquinone oxidoreductase chain 4: D
NADH-ubiquinone oxidoreductase chain 5: E
NADH-ubiquinone oxidoreductase chain 6: F
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7: G
Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I): H
Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I): I
NADH-ubiquinone oxidoreductase-like protein: J
NADH-ubiquinone oxidoreductase chain 4L: K
Acyl carrier protein: L
Complex I-B22: M
Complex I-ESSS: N
NADH-ubiquinone oxidoreductase: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: P
NADH-ubiquinone oxidoreductase-like protein: Q
NADH dehydrogenase (Ubiquinone)-like protein: R
Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I): S
Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I): T
Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I): U
Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I): V
Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I): W
Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I): X
Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I): Y
Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I): Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
8

H
9

I
D

J
J

K
L

L
Q

M
R

N
S

O
U

P
W

Q
X

R
a

S
b

T
c

U
d

V
e

W
g

X
i

Y
j

Z
n

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase subunit 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)

NADH-ubiquinone oxidoreductase-like protein

NADH-ubiquinone oxidoreductase chain 4L

Acyl carrier protein

Complex I-B22

Complex I-ESSS

NADH-ubiquinone oxidoreductase

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH-ubiquinone oxidoreductase-like protein

NADH dehydrogenase (Ubiquinone)-like protein

Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)

Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)

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