SMTL ID : 6qc7.1

Ovine respiratory complex I FRC open class 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: P.204, S.359, C.360, G.361, Q.362, C.363, C.366, T.404, I.405, C.406, L.408 6 PLIP interactions: 6 interactions with chain A, Salt bridges: A:E.189, A:E.189 Metal complexes: A:C.360, A:C.363, A:C.366, A:C.406 SF4.4: 13 residues within 4Å: Chain C: H.101, D.104, C.105, C.108, Q.110, G.111, C.114, L.116, Q.117, R.152, V.205, G.206 Chain D: M.342 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.101, C:C.105, C:C.108, C:C.114 SF4.5: 12 residues within 4Å: Chain C: M.150, C.153, I.154, Q.155, C.156, T.157, C.159, V.183, C.203, P.204, V.205, L.208 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.153, C:C.156, C:C.159, C:C.203 SF4.7: 11 residues within 4Å: Chain D: R.105, H.190 Chain F: A.53, C.54, C.55, G.90, G.117, S.118, C.119, C.149, P.150 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.54, F:C.55, F:C.119, F:C.149 SF4.8: 11 residues within 4Å: Chain G: H.65, V.86, C.87, P.88, K.115, C.116, I.117, Y.118, C.119, C.122, E.133 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.133 Metal complexes: G:C.87, G:C.116, G:C.122 SF4.9: 12 residues within 4Å: Chain G: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, P.127, I.131 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.77, G:C.80, G:C.83, G:C.126

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain A: G.68, R.69, G.70, A.72, K.79, N.97, D.99, G.101, K.107, Y.185, G.188, E.189, E.190, V.223, A.224, N.225, A.407 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.185, A:E.189, A:A.407 Hydrogen bonds: A:R.69, A:R.69, A:D.99, A:G.101, A:K.107, A:V.223, A:N.225 Salt bridges: A:K.79

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

FES.3: 10 residues within 4Å: Chain A: P.103 Chain B: C.103, T.105, P.107, C.108, C.144, L.145, A.147, C.148, M.153 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.103, B:C.108, B:C.144, B:C.148 FES.6: 7 residues within 4Å: Chain C: C.41, Y.42, G.50, C.52, R.53, C.55, C.69 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.41, C:C.52, C:C.55, C:C.69

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 6 residues within 4Å: Chain I: C.59, H.68, V.71, C.84, Y.86, C.87 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.59, I:H.68, I:C.84, I:C.87

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

NDP.11: 19 residues within 4Å: Chain K: T.27, G.28, F.29, L.30, R.50, W.73, V.95, G.96, R.97, F.104, I.132, H.134, Y.145, K.149, P.168, A.169, D.170, I.171, R.177 21 PLIP interactions: 21 interactions with chain K Hydrophobic interactions: K:P.168 Hydrogen bonds: K:T.27, K:T.27, K:T.27, K:G.28, K:F.29, K:L.30, K:R.50, K:V.95, K:V.95, K:Y.145, K:K.149, K:A.169, K:I.171 Salt bridges: K:R.50, K:R.97, K:R.97, K:R.177, K:R.177 pi-Cation interactions: K:R.50, K:R.50

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

ZMP.12: 13 residues within 4Å: Chain N: K.28, V.31, W.38, V.62, M.65, F.66, N.69, A.70, V.78, L.81, F.105 Chain Q: D.43, S.44 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain Q Hydrophobic interactions: N:V.31, N:W.38, N:V.62, N:M.65, N:F.66, N:V.78, N:F.105 Hydrogen bonds: N:K.28, N:F.66, N:N.69, Q:S.44 ZMP.18: 13 residues within 4Å: Chain 0: D.43, S.44 Chain c: H.11, Q.12, L.43, R.46, F.47, H.50, K.51, A.59, L.62, L.63, A.66 9 PLIP interactions: 7 interactions with chain c, 2 interactions with chain 0 Hydrophobic interactions: c:L.43, c:R.46, c:F.47, c:A.59 Hydrogen bonds: c:H.11, c:Q.12, c:H.50, 0:S.44, 0:L.45

3 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.13: 13 residues within 4Å: Chain 9: I.140, W.141 Chain R: L.3 Chain S: M.98, N.99, L.100 Chain T: G.38, G.42, L.45, N.46, G.49, S.50, L.54 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:N.99, S:L.100 3PE.15: 15 residues within 4Å: Chain V: T.166, L.169, Q.170, L.173, Y.174, I.177, M.533, H.534, T.537, P.538, N.541 Chain W: L.405 Chain e: N.87, R.88, D.90 9 PLIP interactions: 7 interactions with chain V, 1 interactions with chain e, 1 interactions with chain W Hydrophobic interactions: V:L.173, V:L.173, V:I.177, W:L.405 Hydrogen bonds: V:Q.170, V:H.534 Salt bridges: V:H.534, V:H.534, e:R.88 3PE.16: 13 residues within 4Å: Chain D: Y.20 Chain V: I.566, S.567, Q.570 Chain W: L.143, L.147, Y.148, F.151, Y.152, A.155 Chain X: I.284, L.288, Y.291 13 PLIP interactions: 4 interactions with chain X, 2 interactions with chain V, 6 interactions with chain W, 1 interactions with chain D Hydrophobic interactions: X:I.284, X:L.288, X:Y.291, X:Y.291, V:I.566, W:Y.148, W:F.151, W:F.151, W:Y.152, W:Y.152, W:A.155 Hydrogen bonds: V:S.567, D:Y.20

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 18 residues within 4Å: Chain V: N.23, F.24, Q.116, K.119, Y.120, L.123, M.150 Chain W: P.353, L.354, A.357, W.358, L.360, L.364, L.369, L.442 Chain Z: D.18, L.22, L.25 11 PLIP interactions: 1 interactions with chain Z, 4 interactions with chain W, 6 interactions with chain V Hydrophobic interactions: Z:L.25, W:W.358, W:L.364, W:L.369, W:L.442, V:F.24, V:L.123 Hydrogen bonds: V:Y.120 Salt bridges: V:K.119, V:K.119, V:K.119

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

PC1.17: 13 residues within 4Å: Chain W: P.159, A.163, Y.166, S.191, F.194, M.195, A.198 Chain X: D.274, I.276, I.277 Chain Y: E.130, G.131, W.132 8 PLIP interactions: 5 interactions with chain W, 1 interactions with chain Y, 2 interactions with chain X Hydrophobic interactions: W:P.159, W:A.163, W:F.194, W:M.195, Y:W.132, X:I.276, X:I.277 Hydrogen bonds: W:S.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Letts, J.A. et al., Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk. Mol.Cell (2019)

Release Date

2019-08-21

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NDUFV2: B
NADH:ubiquinone oxidoreductase core subunit S1: C
NDUFS2: D
NADH:ubiquinone oxidoreductase core subunit S3: E
NDUFS7: F
NDUFS8: G
NDUFV3: H
NDUFS6: I
NADH:ubiquinone oxidoreductase subunit S4: J
NADH:ubiquinone oxidoreductase subunit A9: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: L
NDUFA5: M
NADH:ubiquinone oxidoreductase subunit A6: N
NDUFA7: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: P
Acyl carrier protein: Q0
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 1: S
NADH-ubiquinone oxidoreductase chain 6: T
NADH-ubiquinone oxidoreductase chain 4L: U
NADH-ubiquinone oxidoreductase chain 5: V
NADH-ubiquinone oxidoreductase chain 4: W
NADH-ubiquinone oxidoreductase chain 2: X
NDUFA11: Y
NADH:ubiquinone oxidoreductase subunit B5: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 1
NDUFB10: 2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 3
NADH:ubiquinone oxidoreductase subunit S5: 4
NADH:ubiquinone oxidoreductase subunit A3: 5
NADH:ubiquinone oxidoreductase subunit B3: 6
NADH dehydrogenase [ubiquinone] 1 subunit C2: 7
NADH:ubiquinone oxidoreductase subunit B4: 8
NDUFA13: 9
NDUFB6: a
NADH:ubiquinone oxidoreductase subunit B7: b
NADH:ubiquinone oxidoreductase subunit B9: c
NADH:ubiquinone oxidoreductase subunit B2: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: e
NDUFB11: f
NDUFC1: g
NDUFB1: h
NDUFA1: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V1

B
V2

C
S1

D
S2

E
S3

F
S7

G
S8

H
V3

I
S6

J
S4

K
A9

L
A2

M
A5

N
A6

O
A7

P
AL

Q
AA

0
AB

R
D3

S
D1

T
D6

U
4L

V
D5

W
D4

X
D2

Y
AK

Z
B5

1
A8

2
BJ

3
AJ

4
S5

5
A3

6
B3

7
C2

8
B4

9
AM

a
B6

b
B7

c
B9

d
B2

e
B8

f
BK

g
C1

h
B1

i
A1

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NDUFV2

NADH:ubiquinone oxidoreductase core subunit S1

NDUFS2

NADH:ubiquinone oxidoreductase core subunit S3

NDUFS7

NDUFS8

NDUFV3

NDUFS6

NADH:ubiquinone oxidoreductase subunit S4

NADH:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NDUFA5

NADH:ubiquinone oxidoreductase subunit A6

NDUFA7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

Acyl carrier protein

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

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

NDUFA11

NADH:ubiquinone oxidoreductase subunit B5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NDUFB10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH:ubiquinone oxidoreductase subunit S5

NADH:ubiquinone oxidoreductase subunit A3

NADH:ubiquinone oxidoreductase subunit B3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

NDUFA13

NDUFB6

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

NADH:ubiquinone oxidoreductase subunit B2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NDUFB11

NDUFC1

NDUFB1

NDUFA1

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