SMTL ID : 7zm8.1

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (inhibited by DDM) - 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

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

3PE.1: 9 residues within 4Å: Chain A: F.191, I.193, F.195, I.196, V.326, T.330, F.334, F.345, V.349 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.191, A:I.193, A:F.195, A:F.195, A:I.196, A:T.330, A:F.334, A:F.345, A:V.349 3PE.14: 18 residues within 4Å: Chain E: L.290, L.293, F.294, Q.296, F.420, L.423, K.427, L.431, A.540, S.544, F.554, K.555, F.564, F.567 Chain M: V.23 Chain R: F.127, S.130, F.131 14 PLIP interactions: 2 interactions with chain R, 12 interactions with chain E Hydrophobic interactions: R:F.127, R:F.131, E:F.294, E:F.420, E:F.420, E:L.423, E:A.540, E:F.554, E:F.567, E:F.567 Hydrogen bonds: E:Q.296 Salt bridges: E:K.427, E:K.427, E:K.555 3PE.17: 12 residues within 4Å: Chain D: I.509, Y.510 Chain E: L.10, N.60, I.61, F.62, R.63, N.73, F.122 Chain X: Y.48 Chain Z: Y.69 Ligands: 3PE.31 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.10, E:F.62, E:F.62, E:F.122, D:I.509, D:Y.510, D:Y.510, D:Y.510 Hydrogen bonds: E:N.60, E:R.63, E:N.73 Salt bridges: E:R.63 3PE.19: 9 residues within 4Å: Chain E: F.177, S.206, N.207, I.210, I.211, I.214, C.215, L.276 Ligands: LMT.22 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.177, E:I.210, E:I.211, E:I.214, E:L.276 Hydrogen bonds: E:S.206 3PE.25: 7 residues within 4Å: Chain P: R.23, G.24, L.25, P.30, L.31, G.34, A.35 5 PLIP interactions: 5 interactions with chain P Hydrophobic interactions: P:P.30, P:L.31 Hydrogen bonds: P:G.24 Salt bridges: P:R.23, P:R.23 3PE.26: 15 residues within 4Å: Chain A: I.364, F.368 Chain O: S.140 Chain P: M.39, L.40, W.43, Y.44, V.47, K.48, R.51 Chain W: V.43, L.46, R.47, I.50, D.52 16 PLIP interactions: 5 interactions with chain W, 7 interactions with chain P, 4 interactions with chain A Hydrophobic interactions: W:V.43, W:V.43, W:L.46, W:I.50, P:M.39, P:L.40, P:W.43, P:W.43, P:V.47, A:I.364, A:F.368, A:F.368, A:F.368 Hydrogen bonds: W:D.52 Salt bridges: P:R.51, P:R.51 3PE.31: 13 residues within 4Å: Chain E: L.3, I.6, I.7, L.11, F.76 Chain X: V.45, Y.48, E.51 Chain Z: S.65, F.66, Y.69, N.70 Ligands: 3PE.17 10 PLIP interactions: 6 interactions with chain E, 1 interactions with chain Z, 3 interactions with chain X Hydrophobic interactions: E:L.3, E:L.3, E:I.6, E:I.7, E:L.11, E:F.76, X:V.45, X:Y.48 Hydrogen bonds: Z:N.70, X:E.51

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

PC1.2: 6 residues within 4Å: Chain A: N.45, A.46, V.47, G.48, I.49, L.53 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.53 Hydrogen bonds: A:G.48, A:I.49 PC1.10: 12 residues within 4Å: Chain B: A.34, I.37, L.38, I.73, L.77, I.375, I.543, V.546 Chain Q: Y.89 Chain S: W.49 Ligands: CDL.5, LMT.7 10 PLIP interactions: 6 interactions with chain B, 2 interactions with chain Q, 2 interactions with chain S Hydrophobic interactions: B:I.37, B:L.38, B:L.77, B:I.375, B:I.543, B:V.546, S:W.49, S:W.49 Hydrogen bonds: Q:Y.89, Q:Y.89 PC1.15: 27 residues within 4Å: Chain D: T.407, Q.408, P.411, S.414, L.415, F.418, T.427, P.428, Y.469 Chain E: S.13, G.17, F.18, H.109, R.112, S.115, Y.116, M.123, G.142, V.145, L.149, F.155 Chain X: S.15, P.16, A.17, G.18, G.19, W.20 11 PLIP interactions: 6 interactions with chain E, 3 interactions with chain X, 2 interactions with chain D Hydrophobic interactions: E:F.18, E:F.18, D:T.427 Water bridges: E:R.112 Salt bridges: E:H.109, E:R.112, E:R.112 Hydrogen bonds: X:S.15, X:G.19, X:G.19, D:T.407 PC1.16: 20 residues within 4Å: Chain D: L.334, I.459, Y.467 Chain E: A.159, Q.162, S.163, I.165, S.166, L.169, V.173, M.235, Y.577, N.578, T.582, L.586 Chain R: F.107, S.108, P.109, Y.110, Y.112 14 PLIP interactions: 7 interactions with chain E, 3 interactions with chain R, 4 interactions with chain D Hydrophobic interactions: E:I.165, E:L.169, E:V.173, E:Y.577, E:L.586, R:P.109, D:L.334, D:I.459, D:Y.467, D:Y.467 Hydrogen bonds: E:Q.162, E:N.578, R:Y.110, R:Y.112

14 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 21 residues within 4Å: Chain A: T.85, S.89, M.114, L.115, S.118, A.121, I.125, E.152, L.155, E.201, T.202, N.203, E.211, F.232, F.233, A.235, E.236, S.239, L.242, M.243, L.246 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.114, A:L.115, A:A.121, A:L.155, A:L.242, A:L.246 Hydrogen bonds: A:T.202, A:N.203, A:S.239 LMT.4: 10 residues within 4Å: Chain A: E.31, R.32, Q.39, R.41, D.58, A.59, F.233, L.234, Y.237, R.331 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.58, A:A.59, A:F.233, A:L.234 Hydrogen bonds: A:R.41, A:R.41, A:Y.237, A:R.331 Salt bridges: A:R.32 LMT.6: 13 residues within 4Å: Chain B: N.483, K.486, Y.491 Chain D: V.202, R.203, F.206, Y.207, L.210, Y.211 Chain E: P.606, E.610 Ligands: LMT.18, LMT.29 16 PLIP interactions: 5 interactions with chain B, 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: B:N.483, B:N.483, B:K.486, B:Y.491, B:Y.491, D:R.203 Hydrophobic interactions: D:Y.207, D:L.210, D:L.210, D:Y.211, D:Y.211, D:Y.211, E:P.606, E:P.606 Water bridges: D:V.202 Salt bridges: D:R.203 LMT.7: 13 residues within 4Å: Chain B: T.41, M.42, L.44, S.45, I.69, F.70, I.371, W.557 Chain Q: M.101, S.102 Chain S: W.49 Ligands: LMT.8, PC1.10 10 PLIP interactions: 2 interactions with chain Q, 7 interactions with chain B, 1 interactions with chain S Hydrogen bonds: Q:R.93, B:L.44 Water bridges: Q:S.102 Hydrophobic interactions: B:L.44, B:I.69, B:I.69, B:F.70, B:I.371, B:I.371, S:W.49 LMT.8: 16 residues within 4Å: Chain B: L.44, S.45, F.46, I.47, N.62, M.553, E.556, W.557, M.560 Chain Q: D.19 Chain S: F.46, L.50, I.53, Q.57, M.60 Ligands: LMT.7 10 PLIP interactions: 4 interactions with chain S, 4 interactions with chain B, 2 interactions with chain Q Hydrophobic interactions: S:F.46, S:L.50, S:I.53, B:W.557, B:M.560 Hydrogen bonds: S:Q.57, B:L.44, B:N.62, Q:K.17 Water bridges: Q:D.19 LMT.9: 13 residues within 4Å: Chain B: F.422, Y.423, P.426, L.430, I.434, F.437 Chain D: N.151, K.153, S.154, I.157, I.158, P.187, P.188 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:I.157, D:I.158, D:P.187, B:I.434, B:F.437, B:F.437 Hydrogen bonds: D:K.153, D:K.153 Water bridges: D:S.154 LMT.11: 5 residues within 4Å: Chain C: L.23, I.24, A.26, H.28, P.30 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.23, C:I.24 Hydrogen bonds: C:A.26, C:H.28, C:H.28, C:H.28 Salt bridges: C:H.28 LMT.12: 16 residues within 4Å: Chain A: P.352, A.356 Chain B: V.15, L.17 Chain C: T.99, V.103, L.106, G.107, D.109, H.114 Chain F: R.222 Chain W: L.26, S.29, V.30 Ligands: CDL.27, LMT.30 10 PLIP interactions: 2 interactions with chain W, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: W:L.26, W:V.30, C:T.99, C:V.103, C:V.103, C:L.106 Hydrogen bonds: C:D.109, C:H.114, C:H.114, B:V.15 LMT.13: 6 residues within 4Å: Chain B: L.468 Chain D: T.246, F.250 Chain J: T.122, R.143 Ligands: LMT.21 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain J, 1 interactions with chain D Hydrophobic interactions: B:L.468, J:T.122, D:F.250 Hydrogen bonds: J:R.143 LMT.18: 13 residues within 4Å: Chain E: I.601, L.603, F.604, G.605, G.608, L.609, R.611, G.612, M.667 Chain J: P.107, R.108 Chain Y: W.31 Ligands: LMT.6 8 PLIP interactions: 2 interactions with chain J, 6 interactions with chain E Hydrogen bonds: J:R.108 Salt bridges: J:R.108 Hydrophobic interactions: E:I.601, E:F.604, E:F.604, E:F.604, E:L.609, E:L.609 LMT.21: 13 residues within 4Å: Chain B: L.459, D.460, L.468 Chain D: L.221, S.222, T.225, T.247, F.250, F.253, I.257 Chain J: E.140, R.143 Ligands: LMT.13 9 PLIP interactions: 4 interactions with chain D, 3 interactions with chain J, 2 interactions with chain B Hydrophobic interactions: D:L.221, D:F.253, D:I.257, B:L.468 Hydrogen bonds: D:T.247, J:E.140, J:R.143, B:L.459 Salt bridges: J:R.143 LMT.22: 12 residues within 4Å: Chain D: L.444, M.452 Chain E: A.184, W.187, N.207, I.211 Chain J: Y.185 Chain Y: W.61, L.71, I.72, S.73 Ligands: 3PE.19 12 PLIP interactions: 6 interactions with chain Y, 1 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: Y:W.61, Y:W.61, Y:I.72, D:L.444, E:A.184, E:W.187, E:I.211, E:I.211 Hydrogen bonds: Y:S.73, Y:S.73, E:N.207 Water bridges: Y:I.72 LMT.29: 13 residues within 4Å: Chain B: V.475, I.476, V.479 Chain D: L.214 Chain E: L.609, E.610, L.613, V.614 Chain R: K.46, Y.47, D.51, Y.52 Ligands: LMT.6 13 PLIP interactions: 1 interactions with chain D, 5 interactions with chain E, 4 interactions with chain B, 3 interactions with chain R Hydrophobic interactions: D:L.214, E:L.609, E:E.610, E:L.613, B:V.475, B:I.476, B:V.479, B:V.479 Hydrogen bonds: E:E.610, E:E.610, R:D.51, R:D.51, R:Y.52 LMT.30: 9 residues within 4Å: Chain W: Y.15, C.16, W.18, A.19, R.23, F.27, V.30 Ligands: LMT.12, CDL.27 8 PLIP interactions: 8 interactions with chain W Hydrophobic interactions: W:A.19, W:R.23, W:F.27, W:V.30 Hydrogen bonds: W:Y.15, W:Y.15, W:R.23 Salt bridges: W:R.23

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 30 residues within 4Å: Chain B: L.77, Q.80, F.84, K.88, I.100, F.101, S.533, S.534, P.535, I.538, T.539, I.542 Chain Q: A.54, L.57, M.58, I.61, S.62 Chain S: W.8, F.11, G.12, V.15, R.16, Q.19, R.25, W.34, L.38, F.39, V.42, F.46 Ligands: PC1.10 23 PLIP interactions: 2 interactions with chain Q, 11 interactions with chain S, 10 interactions with chain B Hydrophobic interactions: Q:A.54, Q:L.57, S:W.8, S:F.11, S:F.11, S:V.15, S:L.38, S:F.39, S:F.39, S:F.46, B:L.77, B:F.101, B:P.535, B:I.538, B:I.542 Hydrogen bonds: S:Q.19, B:S.533, B:S.534, B:S.534 Salt bridges: S:R.16, S:R.25, B:K.88, B:K.88 CDL.20: 5 residues within 4Å: Chain A: F.325 Chain I: P.2, V.3, F.5, L.8 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:F.5, I:L.8, A:F.325, A:F.325 Hydrogen bonds: I:P.2, I:V.3 CDL.24: 19 residues within 4Å: Chain D: L.415, F.416, I.419, K.491, F.494, F.495, F.498 Chain E: F.18, F.19 Chain N: L.75, W.76, F.94, W.98 Chain X: W.14, P.16 Chain Z: G.52, A.53, A.54, I.57 25 PLIP interactions: 1 interactions with chain X, 5 interactions with chain N, 9 interactions with chain D, 5 interactions with chain E, 5 interactions with chain Z Hydrophobic interactions: X:P.16, N:F.94, N:F.94, N:W.98, N:W.98, D:L.415, D:F.416, D:I.419, D:F.495, D:F.498, D:F.498, E:F.18, E:F.18, E:F.18, E:F.19, Z:A.54, Z:I.57, Z:I.57 Hydrogen bonds: N:W.76, Z:A.53, Z:A.54 Salt bridges: D:K.491, D:K.491, D:K.491, E:K.22 CDL.27: 16 residues within 4Å: Chain B: S.8, L.11, S.12, V.15 Chain C: T.99, I.100 Chain Q: K.73, R.76, L.77, F.80 Chain W: R.7, F.8, W.9, Y.15 Ligands: LMT.12, LMT.30 11 PLIP interactions: 4 interactions with chain W, 5 interactions with chain Q, 2 interactions with chain C Hydrophobic interactions: W:F.8, W:F.8, W:W.9, Q:L.77, Q:F.80, C:T.99, C:I.100 Hydrogen bonds: W:F.8, Q:R.76 Salt bridges: Q:K.73, Q:R.76 CDL.28: 21 residues within 4Å: Chain A: Y.366 Chain B: M.3 Chain C: A.85, Y.86, A.89, L.92, I.93 Chain F: I.201 Chain Q: H.28, 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 26 PLIP interactions: 4 interactions with chain W, 12 interactions with chain Q, 8 interactions with chain C, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: W:P.37, W:L.40, W:L.40, W:A.41, Q:P.154, Q:W.155, Q:W.155, Q:F.156, Q:F.158, Q:F.158, Q:F.158, C:A.85, C:Y.86, C:A.89, C:L.92, C:L.92, C:I.93, C:I.93, C:I.93, F:I.201, A:Y.366 Hydrogen bonds: Q:R.130, Q:N.160 Salt bridges: Q:R.130, Q:R.130, Q:R.130

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

ZMP.23: 20 residues within 4Å: Chain E: F.556 Chain L: S.98 Chain M: R.4, A.7, L.8, A.14, L.17, I.35, L.38, F.39, N.42, R.43, V.45, Q.51, L.54, T.58, L.62, W.65 Chain T: F.19, F.24 14 PLIP interactions: 12 interactions with chain M, 1 interactions with chain E, 1 interactions with chain T Hydrophobic interactions: M:R.4, M:A.7, M:A.14, M:L.17, M:I.35, M:I.35, M:L.38, M:L.38, M:W.65, E:F.556, T:F.24 Hydrogen bonds: M:T.58 Salt bridges: M:R.4, 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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