SMTL ID : 8ibe.1

Respiratory complex Peripheral Arm of CI, focus-refined map of type II, Wild type mouse under cold temperature

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-mer

Ligands

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine

3PE.1: 15 residues within 4Å: Chain A: S.99, L.102, A.103, W.106, T.107 Chain H: H.287, K.291, P.295 Chain T: L.9, E.16, L.19, V.20, S.22, F.23, W.26 16 PLIP interactions: 10 interactions with chain T, 3 interactions with chain H, 3 interactions with chain A Hydrophobic interactions: T:L.9, T:E.16, T:L.19, T:F.23, T:F.23, T:F.23, T:F.23, T:F.23, T:W.26, T:W.26, H:P.295, H:P.295, A:L.102, A:A.103, A:W.106 Salt bridges: H:K.291 3PE.13: 17 residues within 4Å: Chain A: L.3, Y.4, I.7, F.8, I.11 Chain H: T.76, L.77, T.80, L.81, N.97, L.98, N.99, F.104, T.108 Chain R: F.140, T.141, Y.143 12 PLIP interactions: 6 interactions with chain A, 5 interactions with chain H, 1 interactions with chain S Hydrophobic interactions: A:L.3, A:Y.4, A:Y.4, A:F.8, A:F.8, A:I.11, H:L.77, H:T.80, H:L.81, H:F.104 Hydrogen bonds: H:N.99, S:A.39 3PE.14: 24 residues within 4Å: Chain D: R.266 Chain H: W.179, P.180, M.183, F.186, I.187, P.197, F.198, L.266, Y.277, F.280, H.287, L.288, N.292, F.293, L.296, L.300 Chain I: I.60, L.61, W.63 Chain R: I.40, L.43 Chain T: V.21, V.25 25 PLIP interactions: 18 interactions with chain H, 1 interactions with chain R, 2 interactions with chain I, 2 interactions with chain D, 2 interactions with chain T Hydrophobic interactions: H:W.179, H:P.180, H:M.183, H:F.186, H:F.186, H:I.187, H:P.197, H:F.198, H:L.266, H:Y.277, H:F.280, H:F.280, H:L.288, H:F.293, H:L.296, H:L.300, R:I.40, I:L.61, I:W.63, T:V.21, T:V.25 Hydrogen bonds: H:H.287, H:N.292 Salt bridges: D:R.266, D:R.266

6 x SF4: IRON/SULFUR CLUSTER

SF4.2: 10 residues within 4Å: Chain B: C.99, C.100, G.135, T.136, S.163, C.164, C.194, P.195 Chain D: R.138, H.223 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.99, B:C.100, B:C.164, B:C.194, B:C.194 SF4.8: 12 residues within 4Å: Chain F: I.205, P.223, S.378, C.379, G.380, Q.381, C.382, C.385, T.423, C.425, L.427, G.428 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.379, F:C.382, F:C.385, F:C.425 SF4.9: 8 residues within 4Å: Chain G: H.124, D.127, C.128, C.131, Q.133, C.137, V.228, G.229 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.127 Metal complexes: G:H.124, G:C.128, G:C.131, G:C.137 SF4.10: 9 residues within 4Å: Chain G: M.173, C.176, I.177, C.179, T.180, R.181, C.182, C.226, L.231 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.176, G:C.179, G:C.182, G:C.226 SF4.15: 10 residues within 4Å: Chain I: H.101, C.123, I.128, C.152, I.153, Y.154, C.155, G.156, C.158, E.169 5 PLIP interactions: 5 interactions with chain I, Salt bridges: I:E.169 Metal complexes: I:C.123, I:C.152, I:C.155, I:C.158 SF4.16: 9 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, C.119, I.130, C.162, A.166, I.167 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.113, I:C.116, I:C.119, I:C.162

1 x UQ1: UBIQUINONE-1

UQ1.3: 9 residues within 4Å: Chain B: M.93, T.94, F.121, R.122, A.123 Chain D: Q.87, L.192, D.193 Chain H: E.204 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.93, B:R.122

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

PC1.4: 13 residues within 4Å: Chain B: K.77, D.80, L.81, W.84, R.87, K.213 Chain H: I.39, V.40, L.46, F.49 Chain U: R.29, W.75, V.77 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:D.80, B:L.81, B:W.84, B:W.84, B:W.84, B:W.84, H:L.46, H:F.49 Salt bridges: B:R.87, B:R.87, B:K.213, B:K.213 PC1.5: 14 residues within 4Å: Chain A: L.24, P.25, Q.26, Y.30 Chain B: I.82, E.154, L.218, W.221 Chain H: F.49, A.52, M.53, M.57 Chain J: D.90, F.310 13 PLIP interactions: 3 interactions with chain H, 5 interactions with chain B, 3 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: H:F.49, H:A.52, H:M.53, B:I.82, B:W.221, B:W.221, B:W.221, J:F.310, J:F.310, A:L.24, A:L.24 Salt bridges: B:E.154 Hydrogen bonds: J:D.90

2 x FES: FE2/S2 (INORGANIC) CLUSTER

FES.6: 10 residues within 4Å: Chain E: C.134, T.136, P.138, C.139, C.175, L.176, G.177, A.178, C.179, M.184 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.134, E:C.139, E:C.175, E:C.179 FES.11: 9 residues within 4Å: Chain G: R.62, F.63, C.64, Y.65, G.73, C.75, R.76, C.78, C.92 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:F.63, G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE

FMN.7: 19 residues within 4Å: Chain F: G.87, R.88, G.89, A.91, K.98, N.116, D.118, E.119, G.120, Y.204, I.205, G.207, E.208, E.209, A.243, N.244, T.247, A.426, L.427 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:Y.204, F:I.205, F:E.208, F:A.426, F:L.427 Hydrogen bonds: F:G.89, F:N.116, F:E.119, F:G.120, F:G.207, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247, F:T.247

1 x UQ9: Ubiquinone-9

UQ9.12: 18 residues within 4Å: Chain B: W.91, A.123 Chain H: V.11, L.14, I.15, M.17, A.18, T.21, R.25, P.48, D.51, A.52, L.55, E.202, F.224, M.225, Y.228, R.274 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: H:V.11, H:L.14, H:I.15, H:A.18, H:P.48, H:A.52, H:L.55, H:F.224, H:F.224, B:W.91, B:W.91 Hydrogen bonds: H:E.202, H:R.274

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NDP.17: 23 residues within 4Å: Chain B: R.224 Chain J: G.60, T.62, G.63, F.64, L.65, R.85, C.86, W.108, L.129, I.130, G.131, R.132, F.139, V.144, F.145, V.167, H.169, K.184, P.203, S.204, I.206, R.212 21 PLIP interactions: 20 interactions with chain J, 1 interactions with chain B Hydrophobic interactions: J:P.203, J:I.206, J:I.206 Hydrogen bonds: J:G.60, J:T.62, J:T.62, J:T.62, J:F.64, J:L.65, J:L.129, J:G.131, J:K.184, J:I.206, J:I.206 Salt bridges: J:R.85, J:R.132, J:R.132, J:R.212, J:R.212, B:R.224 pi-Cation interactions: J:R.85

1 x ZN: ZINC ION

ZN.18: 4 residues within 4Å: Chain L: C.79, H.88, C.104, C.107 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.79, L:H.88, L:C.104, L:C.107

1 x EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate

EHZ.19: 16 residues within 4Å: Chain N: S.112 Chain P: L.28, K.32, V.35, W.42, M.69, F.70, N.73, A.74, H.75, V.76, V.82, L.85, G.89, E.92, F.109 14 PLIP interactions: 13 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: P:L.28, P:K.32, P:W.42, P:W.42, P:M.69, P:N.73, P:V.82, P:F.109, P:F.109 Hydrogen bonds: P:W.42, P:N.73, P:N.73, N:S.112 Salt bridges: P:K.32

1 x CDL: CARDIOLIPIN

CDL.20: 18 residues within 4Å: Chain H: Y.43 Chain S: M.1, W.2, F.3, L.6, P.7, A.10 Chain U: E.2, L.3, V.6, L.7, R.9, G.10, Q.13 Chain V: A.4, T.5, V.7, I.8 14 PLIP interactions: 2 interactions with chain H, 3 interactions with chain U, 6 interactions with chain S, 3 interactions with chain V Hydrophobic interactions: H:Y.43, H:Y.43, U:L.3, S:W.2, S:F.3, S:F.3, S:L.6, S:P.7, S:A.10, V:V.7 Hydrogen bonds: U:Q.13, V:T.5, V:T.5 Salt bridges: U:R.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, Y.C. et al., Structural basis of respiratory complex adaptation to cold temperatures. Cell (2024)

Release Date

2024-09-18

Peptides

NADH-ubiquinone oxidoreductase chain 3: A
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial: B
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial: C
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial: D
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: E
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: F
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial: G
NADH-ubiquinone oxidoreductase chain 1: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial: I
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial: J
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial: K
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: M
Acyl carrier protein, mitochondrial: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6: P
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: R
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: S
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: T
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: U
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: V
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
P

K
Q

L
R

M
S

N
T

O
V

P
W

Q
X

R
Z

S
a

T
b

U
q

V
r

W
s

Membrane

We predict this structure to be a membrane protein.
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NADH-ubiquinone oxidoreductase chain 3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

Acyl carrier protein, mitochondrial

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

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