SMTL ID : 7zmh.1

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 1) - 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

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

3PE.1: 11 residues within 4Å: Chain A: P.189, F.191, I.192, F.195, I.196, P.206, L.323, V.326, T.330, F.345, V.349 Ligand excluded by PLIP 3PE.6: 16 residues within 4Å: Chain B: P.426, L.430, I.434, P.444, L.548 Chain D: S.19, K.153, S.154, I.157, I.158, L.161, L.165, S.184, P.187, P.188, I.191 Ligand excluded by PLIP 3PE.9: 8 residues within 4Å: Chain D: I.10, I.13, L.17, Y.74, K.77, I.81, T.82, L.85 Ligand excluded by PLIP 3PE.11: 12 residues within 4Å: Chain B: P.259, L.321, I.325 Chain E: L.623, Y.634, V.637, L.641, L.655, L.662 Chain J: R.38, L.41, R.43 Ligand excluded by PLIP 3PE.12: 9 residues within 4Å: Chain D: I.506, Y.510 Chain E: I.61, F.62, R.63, N.73 Chain Z: Y.69 Ligands: PC1.22, 3PE.33 Ligand excluded by PLIP 3PE.13: 15 residues within 4Å: Chain B: I.324, I.469 Chain E: L.603, F.604, G.605, G.608, L.609, R.611, G.612, L.613, K.615, M.667 Chain J: R.108 Ligands: PC1.8, 3PE.19 Ligand excluded by PLIP 3PE.14: 19 residues within 4Å: Chain E: L.290, L.293, F.294, Q.296, I.413, F.420, K.427, L.431, I.539, V.551, F.554, K.555, F.564, F.567 Chain M: V.23, H.24 Chain R: F.127, S.130, F.131 Ligand excluded by PLIP 3PE.16: 8 residues within 4Å: Chain E: R.558, N.562, I.563, F.566 Chain R: K.119, Q.123, L.126, F.127 Ligand excluded by PLIP 3PE.17: 13 residues within 4Å: Chain A: I.87, F.88, L.91, N.105, L.107, Y.113 Chain C: S.2, M.4, I.8 Chain F: F.59, I.62, L.63, N.67 Ligand excluded by PLIP 3PE.19: 10 residues within 4Å: Chain E: F.604, R.611 Chain J: R.105, P.107, R.108, G.111, F.112, A.114 Chain Y: W.31 Ligands: 3PE.13 Ligand excluded by PLIP 3PE.23: 8 residues within 4Å: Chain P: R.23, G.24, L.25, R.27, P.30, L.31, G.34, A.35 Ligand excluded by PLIP 3PE.24: 15 residues within 4Å: Chain A: P.186, L.187, L.357, V.361, I.364, F.368 Chain P: M.39, W.43, Y.44, V.47, K.48 Chain W: L.46, R.47, I.50, D.52 Ligand excluded by PLIP 3PE.29: 16 residues within 4Å: Chain A: P.352, A.356 Chain C: T.99, V.103, L.106 Chain W: F.8, Y.15, C.16, W.18, R.23, L.26, F.27, S.29, V.30, G.33 Ligands: CDL.25 Ligand excluded by PLIP 3PE.30: 3 residues within 4Å: Chain W: R.17, R.21, F.28 Ligand excluded by PLIP 3PE.31: 7 residues within 4Å: Chain E: F.47, F.48, F.480 Chain G: Y.45, L.47 Chain X: D.62, F.64 Ligand excluded by PLIP 3PE.33: 20 residues within 4Å: Chain D: L.429 Chain E: L.3, I.7, L.10, L.11, V.14, I.61, F.122, M.123 Chain X: V.37, I.41, Y.48, E.51, H.52 Chain Z: F.66, Y.69, N.70 Ligands: 3PE.12, CDL.21, PC1.22 Ligand excluded by PLIP 3PE.34: 10 residues within 4Å: Chain D: I.92 Chain N: Y.95, G.99, S.100, V.103, F.104, A.107 Chain Z: F.87, I.90, Y.93 Ligand excluded by PLIP

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

PC1.2: 5 residues within 4Å: Chain A: Y.26, A.46, G.48, I.49, L.53 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.53 Hydrogen bonds: A:A.46, A:G.48, A:I.49 PC1.5: 3 residues within 4Å: Chain C: I.24, F.25, H.28 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.25, C:F.25 PC1.8: 21 residues within 4Å: Chain B: L.331, I.472, I.476, V.479, N.483, K.486 Chain D: V.202, R.203, F.206, Y.207, L.210, Y.211, L.214, I.257 Chain E: G.605, P.606, L.609, E.610, L.613, V.614 Ligands: 3PE.13 22 PLIP interactions: 5 interactions with chain B, 11 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: B:L.331, B:I.472, B:I.476, B:V.479, D:F.206, D:Y.207, D:L.210, D:L.210, D:Y.211, D:Y.211, D:L.214, D:I.257, E:P.606, E:P.606, E:L.609, E:L.609, E:E.610, E:V.614 Hydrogen bonds: B:N.483 Water bridges: D:R.203 Salt bridges: D:R.203, D:R.203 PC1.10: 32 residues within 4Å: Chain D: T.407, Q.408, P.411, S.414, L.415, F.418, I.419, T.427, P.428, L.429, Y.469 Chain E: S.13, G.17, F.18, H.109, R.112, S.115, Y.116, L.119, M.123, V.138, E.141, G.142, V.145, L.149, F.155 Chain X: S.15, A.17, G.18, G.19, W.20 Ligands: CDL.21 24 PLIP interactions: 7 interactions with chain D, 13 interactions with chain E, 4 interactions with chain X Hydrophobic interactions: D:T.407, D:L.415, D:F.418, D:I.419, D:I.419, D:P.428, D:L.429, E:F.18, E:F.18, E:R.112, E:Y.116, E:L.119, E:E.141, E:V.145, E:L.149, E:L.149 Water bridges: E:R.112 Salt bridges: E:H.109, E:R.112, E:R.112 Hydrogen bonds: X:S.15, X:A.17, X:G.19, X:G.19 PC1.15: 17 residues within 4Å: Chain D: L.334, F.460, Y.467 Chain E: A.159, Q.162, S.166, L.169, T.170, L.229, M.235, Y.577, N.578, T.582 Chain R: F.107, P.109, Y.110, Y.112 11 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D, 2 interactions with chain R Hydrophobic interactions: E:L.169, E:L.169, E:Y.577, E:Y.577, E:T.582, D:L.334, D:F.460, D:Y.467 Hydrogen bonds: E:N.578, R:Y.110, R:Y.112 PC1.22: 22 residues within 4Å: Chain D: Y.128, L.131, L.132, L.374, F.378, F.503, I.506, F.513 Chain N: W.98, L.101, F.104, A.105, Y.108, A.109, K.111, D.113 Chain Z: S.65, Y.69, R.73 Ligands: 3PE.12, CDL.21, 3PE.33 14 PLIP interactions: 4 interactions with chain N, 8 interactions with chain D, 2 interactions with chain Z Hydrophobic interactions: N:W.98, N:L.101, N:F.104, D:L.131, D:L.374, D:F.378, D:F.503, D:I.506, D:F.513, D:F.513, D:F.513, Z:Y.69 Salt bridges: N:D.113, Z:R.73 PC1.27: 14 residues within 4Å: Chain B: A.34, Y.35, L.38 Chain Q: A.42, H.43, A.46, A.47, A.49, A.50, A.53, A.54, Y.89 Ligands: CDL.3, PC1.28 6 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain B Hydrophobic interactions: Q:A.46, Q:A.49, Q:A.53, B:A.34, B:Y.35, B:Y.35 PC1.28: 9 residues within 4Å: Chain B: A.34, L.38, T.41, I.73, I.76 Chain Q: H.43, Y.89 Ligands: LMN.4, PC1.27 5 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain B Hydrogen bonds: Q:Y.89, Q:Y.89 Hydrophobic interactions: B:A.34, B:I.73, B:I.76

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 33 residues within 4Å: Chain B: L.77, Q.80, F.84, K.88, W.90, F.101, S.533, S.534, P.535, I.538, T.539, I.542, V.546 Chain Q: A.53, A.54, L.57, M.58, I.61, S.62 Chain S: W.8, F.11, G.12, R.16, Q.19, R.25, W.34, L.38, F.39, V.42, G.43, F.46 Ligands: LMN.4, PC1.27 29 PLIP interactions: 13 interactions with chain B, 3 interactions with chain Q, 13 interactions with chain S Hydrophobic interactions: B:L.77, B:F.101, B:F.101, B:I.538, B:I.538, B:T.539, B:I.542, B:I.542, B:V.546, Q:A.53, Q:A.54, Q:L.57, S:W.8, S:F.11, S:W.34, S:F.39, S:F.39, S:F.39, S:F.39, S:V.42, S:F.46, S:F.46 Hydrogen bonds: B:S.534, B:S.534, S:Q.19 Salt bridges: B:K.88, B:K.88, S:R.16, S:R.25 CDL.18: 4 residues within 4Å: Chain A: F.325 Chain I: P.2, V.3, Y.11 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:V.3, I:V.3, I:Y.11, A:F.325, A:F.325 Hydrogen bonds: I:V.3 CDL.21: 23 residues within 4Å: Chain D: L.412, F.416, K.491, F.494, F.495, F.498, S.502, I.506 Chain E: F.18 Chain N: L.75, W.76, F.94, Y.95, W.98 Chain X: W.14, P.16 Chain Z: G.52, A.53, A.54, I.57 Ligands: PC1.10, PC1.22, 3PE.33 24 PLIP interactions: 7 interactions with chain N, 1 interactions with chain X, 4 interactions with chain Z, 8 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: N:F.94, N:Y.95, N:W.98, N:W.98, N:W.98, N:W.98, X:P.16, Z:A.54, Z:I.57, D:F.416, D:F.494, D:F.494, D:F.498, D:F.498, D:F.498, D:I.506, E:F.18, E:F.18 Hydrogen bonds: N:W.76, Z:A.53, Z:A.54 Salt bridges: D:K.491, E:K.22 Water bridges: E:K.22 CDL.25: 20 residues within 4Å: Chain B: L.7, S.8, L.11, S.12, V.15 Chain C: G.96, T.99, I.100 Chain Q: K.73, R.76, L.77, F.80 Chain W: R.7, F.8, W.9, Y.15, V.30, A.34 Ligands: CDL.26, 3PE.29 20 PLIP interactions: 2 interactions with chain C, 9 interactions with chain Q, 6 interactions with chain W, 3 interactions with chain B Hydrophobic interactions: C:T.99, C:I.100, Q:L.77, Q:F.80, Q:F.80, Q:F.80, W:F.8, W:F.8, W:V.30, W:A.34, B:L.7, B:L.11, B:V.15 Hydrogen bonds: Q:K.73, Q:K.73, W:F.8 Water bridges: Q:L.77, W:W.9 Salt bridges: Q:K.73, Q:R.76 CDL.26: 24 residues within 4Å: Chain A: Y.366 Chain B: L.7 Chain C: A.85, Y.86, A.89, L.92, I.93, G.96, I.97, I.100 Chain Q: H.28, E.128, S.129, R.130, L.131, P.154, W.155, F.158, V.159, N.160 Chain W: P.37, L.40, A.41 Ligands: CDL.25 24 PLIP interactions: 7 interactions with chain C, 13 interactions with chain Q, 3 interactions with chain W, 1 interactions with chain B Hydrophobic interactions: C:A.85, C:L.92, C:L.92, C:I.93, C:I.93, C:I.97, C:I.100, Q:W.155, Q:W.155, Q:F.158, Q:F.158, Q:F.158, W:P.37, W:L.40, W:A.41, B:L.7 Hydrogen bonds: Q:E.128, Q:R.130, Q:R.130, Q:F.158, Q:N.160 Salt bridges: Q:R.130, Q:R.130, Q:R.130

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

LMN.4: 21 residues within 4Å: Chain B: T.41, L.44, F.46, I.47, N.62, I.66, I.371, E.556, W.557, M.560, I.563, L.564, I.567 Chain S: W.8, F.46, W.49, I.53, K.56, M.60 Ligands: CDL.3, PC1.28 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain S Hydrophobic interactions: B:I.66, B:I.66, B:I.371, B:I.371, B:W.557, B:W.557, S:W.8, S:F.46, S:W.49, S:I.53 Hydrogen bonds: B:L.44, B:L.44, B:M.560 Salt bridges: S:K.56 LMN.7: 15 residues within 4Å: Chain B: I.464, L.468 Chain D: F.218, L.221, T.225, E.244, T.246, T.247, F.250, F.253, G.254, I.257 Chain J: T.122, Y.125, R.143 15 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B, 5 interactions with chain J Hydrophobic interactions: D:F.218, D:T.225, D:F.250, D:F.250, D:I.257, B:L.468, J:T.122, J:Y.125 Hydrogen bonds: D:E.244, D:T.247, D:T.247, B:D.460, J:Y.125, J:R.143, J:R.143 LMN.32: 17 residues within 4Å: Chain D: L.444, P.448, M.452 Chain E: V.180, A.184, W.187, N.207, I.211 Chain J: K.184, Y.185, V.187 Chain Y: K.56, L.60, W.61, L.63, I.72, S.73 17 PLIP interactions: 2 interactions with chain J, 4 interactions with chain E, 2 interactions with chain D, 9 interactions with chain Y Hydrogen bonds: J:K.184, J:K.184, E:N.207, Y:K.56, Y:K.56, Y:W.61 Hydrophobic interactions: E:V.180, E:A.184, E:W.187, D:L.444, D:P.448, Y:W.61, Y:W.61, Y:W.61, Y:W.61, Y:L.63, Y:I.72

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

ZMP.20: 20 residues within 4Å: Chain E: F.556 Chain L: D.97, S.98, L.99 Chain M: A.7, L.8, L.17, I.35, L.38, F.39, N.42, R.43, Q.51, L.54, L.55, T.58, L.61, L.62 Chain T: T.17, F.19 15 PLIP interactions: 10 interactions with chain M, 1 interactions with chain T, 1 interactions with chain E, 3 interactions with chain L Hydrophobic interactions: M:L.8, M:L.17, M:I.35, M:L.38, M:F.39, M:Q.51, M:L.61, M:L.62, T:F.19, E:F.556 Hydrogen bonds: M:N.42, L:D.97, L:S.98, L:L.99 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.
Show / Hide

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)

Related Entries With Identical Sequence