SMTL ID : 6qc5.1

Ovine respiratory complex I FRC closed class 1

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 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.189 Metal complexes: A:C.360, A:C.363, A:C.366, A:C.406 SF4.4: 12 residues within 4Å: Chain C: H.101, D.104, C.105, C.108, Q.110, 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: 11 residues within 4Å: Chain C: C.153, I.154, Q.155, C.156, T.157, R.158, C.159, 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 SF4.8: 11 residues within 4Å: Chain D: R.105 Chain F: A.53, C.54, C.55, G.90, T.91, 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 SF4.9: 10 residues within 4Å: Chain G: H.65, C.87, P.88, I.92, C.116, I.117, Y.118, C.119, G.120, C.122 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.133 Metal complexes: G:C.87, G:C.116, G:C.122 SF4.10: 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: 18 residues within 4Å: Chain A: G.68, R.69, G.70, F.74, T.76, K.79, N.97, D.99, E.100, G.101, K.107, Y.185, G.188, E.189, E.190, V.223, N.225, T.228 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.189 Hydrogen bonds: A:R.69, A:R.69, A:G.70, A:F.74, A:N.97, A:G.101, A:K.107, A:K.107, A:N.225, A:T.228 Salt bridges: A:K.79

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

FES.3: 10 residues within 4Å: Chain B: C.103, T.104, T.105, T.106, P.107, C.108, C.144, L.145, 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: 8 residues within 4Å: Chain C: C.41, Y.42, G.50, N.51, 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

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

3PE.7: 17 residues within 4Å: Chain D: W.10, Q.13, Y.14 Chain W: L.562, I.566, S.567, Q.570 Chain X: N.144, L.147, Y.148, F.151, Y.152, A.155, L.212 Chain Y: L.287, L.288, Y.291 12 PLIP interactions: 6 interactions with chain X, 1 interactions with chain W, 3 interactions with chain Y, 2 interactions with chain D Hydrophobic interactions: X:Y.148, X:F.151, X:F.151, X:F.151, X:L.212, W:L.562, Y:L.287, Y:L.288, Y:Y.291 Hydrogen bonds: X:N.144, D:Y.14, D:Y.14 3PE.14: 16 residues within 4Å: Chain W: D.163, T.166, L.169, Q.170, L.173, Y.174, L.229, Y.529, H.534, T.537, P.538, N.541 Chain X: L.405 Chain e: N.87, R.88, D.90 9 PLIP interactions: 6 interactions with chain W, 2 interactions with chain X, 1 interactions with chain e Hydrophobic interactions: W:L.173, W:L.229, W:P.538, X:L.405, X:L.405 Hydrogen bonds: W:Q.170 Salt bridges: W:H.534, W:H.534, e:R.88

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 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.12: 23 residues within 4Å: Chain F: R.179 Chain K: T.27, G.28, F.29, L.30, R.50, C.51, W.73, L.94, V.95, G.96, R.97, E.98, F.104, I.132, S.133, H.134, Y.145, K.149, P.168, A.169, D.170, R.177 18 PLIP interactions: 17 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:T.27, K:T.27, K:T.27, K:G.28, K:F.29, K:R.50, K:V.95, K:E.98, K:K.149, K:P.168, K:D.170 Salt bridges: K:R.50, K:R.97, K:R.177, F:R.179 pi-Cation interactions: K:R.50, K:R.50, K:K.149

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

ZMP.13: 13 residues within 4Å: Chain N: V.31, R.32, W.38, V.62, M.65, F.66, N.69, A.70, V.72, L.81 Chain Q: D.43, S.44, L.45 9 PLIP interactions: 7 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: N:W.38, N:W.38, N:V.62, N:L.81 Hydrogen bonds: N:R.32, N:F.66, N:N.69, Q:S.44, Q:L.45 ZMP.16: 16 residues within 4Å: Chain 1: D.43, S.44, L.45 Chain c: H.11, Q.12, L.43, R.46, F.47, H.50, K.51, E.53, A.59, L.62, L.63, A.66, E.69 12 PLIP interactions: 10 interactions with chain c, 2 interactions with chain 1 Hydrophobic interactions: c:Q.12, c:L.43, c:R.46, c:F.47, c:A.59, c:E.69 Hydrogen bonds: c:Q.12, c:H.50, c:H.50, c:E.53, 1:S.44, 1:L.45

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

PC1.15: 8 residues within 4Å: Chain X: A.163, Y.166, S.191, M.195, A.198 Chain Y: I.276, I.277 Chain Z: W.132 8 PLIP interactions: 2 interactions with chain Y, 5 interactions with chain X, 1 interactions with chain Z Hydrophobic interactions: Y:I.276, Y:I.277, X:A.163, X:M.195, Z:W.132 Hydrogen bonds: X:Y.166, X:Y.166, X: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,NADH:ubiquinone oxidoreductase core subunit S2: D
NADH:ubiquinone oxidoreductase core subunit S3: E
NADH:ubiquinone oxidoreductase core subunit S7,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: Q1
NDUFA13: R
NADH-ubiquinone oxidoreductase chain 3: S
NADH-ubiquinone oxidoreductase chain 1: T
NADH-ubiquinone oxidoreductase chain 6: U
NADH-ubiquinone oxidoreductase chain 4L: V
NADH-ubiquinone oxidoreductase chain 5: W
NADH-ubiquinone oxidoreductase chain 4: X
NADH-ubiquinone oxidoreductase chain 2: Y
NDUFA11: Z
NADH:ubiquinone oxidoreductase subunit B5: 0
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 2
NDUFB10: 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 4
NADH:ubiquinone oxidoreductase subunit S5: 5
NADH:ubiquinone oxidoreductase subunit A3: 6
NADH:ubiquinone oxidoreductase subunit B3: 7
NADH dehydrogenase [ubiquinone] 1 subunit C2: 8
NADH:ubiquinone oxidoreductase subunit B4: 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

1
AB

R
AM

S
D3

T
D1

U
D6

V
4L

W
D5

X
D4

Y
D2

Z
AK

0
B5

2
A8

3
BJ

4
AJ

5
S5

6
A3

7
B3

8
C2

9
B4

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 S2

NADH:ubiquinone oxidoreductase core subunit S3

NADH:ubiquinone oxidoreductase core subunit S7,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

NDUFA13

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

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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