SMTL ID : 8ic3.1

Respiratory complex Peripheral Arm of CI, focus-refined map of type I, PERK -/- 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

6 x SF4: IRON/SULFUR CLUSTER

SF4.1: 12 residues within 4Å: Chain B: A.98, C.99, C.100, G.135, T.136, G.162, S.163, C.164, C.194, P.195 Chain D: R.138, H.223 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:C.99, B:C.100, B:C.164, B:C.194, B:C.194, B:C.194 SF4.6: 11 residues within 4Å: Chain F: I.205, 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 SF4.7: 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 SF4.8: 8 residues within 4Å: Chain G: M.173, C.176, I.177, C.179, T.180, 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 SF4.14: 11 residues within 4Å: Chain I: H.101, C.123, P.124, 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 SF4.15: 11 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, C.119, Y.145, C.162, P.163, 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

UQ1.2: 9 residues within 4Å: Chain B: T.94, M.104, M.114, F.121, R.122, A.123 Chain D: L.192 Chain H: E.204 Ligands: UQ9.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:T.94, B:F.121 pi-Stacking: B:F.121 Hydrogen bonds: H:E.204

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

PC1.3: 10 residues within 4Å: Chain B: K.77, D.80, L.81, W.84, R.87 Chain H: I.39, L.46 Chain U: R.29, W.75, V.77 9 PLIP interactions: 1 interactions with chain U, 7 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: U:W.75, B:K.77, B:D.80, B:L.81, B:L.81, B:L.81, B:W.84, H:L.46 Salt bridges: B:R.87 PC1.13: 20 residues within 4Å: Chain H: L.175, M.183, W.272 Chain I: D.55, R.59, M.62, T.64, E.65, I.67, R.68, L.70, G.71 Chain R: R.28, G.29, L.30, G.32, M.35 Chain V: W.14, A.15 Ligands: 3PE.12 8 PLIP interactions: 1 interactions with chain R, 4 interactions with chain I, 2 interactions with chain H, 1 interactions with chain V Salt bridges: R:R.28 Hydrophobic interactions: I:T.64, I:I.67, I:L.70, H:L.175, H:W.272, V:W.14 Hydrogen bonds: I:T.64

2 x FES: FE2/S2 (INORGANIC) CLUSTER

FES.4: 11 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 Chain F: G.123 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.134, E:C.139, E:C.179 FES.9: 8 residues within 4Å: Chain G: R.62, C.64, Y.65, G.73, C.75, R.76, C.78, C.92 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.64, G:C.75, G:C.78, G:C.92

1 x FMN: FLAVIN MONONUCLEOTIDE

FMN.5: 19 residues within 4Å: Chain F: G.87, R.88, G.89, A.91, K.98, N.116, D.118, G.120, Y.204, I.205, G.207, E.208, E.209, V.242, A.243, N.244, T.247, A.426, L.427 15 PLIP interactions: 15 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:D.118, F:G.120, F:G.207, F:E.209, F:N.244, F:N.244, F:T.247, F:T.247

1 x UQ9: Ubiquinone-9

UQ9.10: 20 residues within 4Å: Chain B: D.115, F.121, R.122 Chain D: M.197 Chain H: M.17, A.18, T.21, R.25, L.28, R.34, P.48, D.51, A.52, L.55, A.221, F.224, M.225, Y.228, R.274 Ligands: UQ1.2 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:A.18, H:T.21, H:A.52, H:L.55, H:A.221, H:F.224, H:F.224, H:F.224 Hydrogen bonds: H:R.274

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

3PE.11: 18 residues within 4Å: Chain A: M.1, L.3, Y.4, I.7, F.8, I.11 Chain H: L.81, S.84, N.97, L.98, N.99, F.104, T.108 Chain R: F.140, T.141, W.142, Y.143 Chain S: A.39 14 PLIP interactions: 9 interactions with chain A, 4 interactions with chain H, 1 interactions with chain S Hydrophobic interactions: A:L.3, A:L.3, A:Y.4, A:Y.4, A:Y.4, A:I.7, A:I.7, A:F.8, A:I.11, H:L.81, H:F.104, H:F.104 Hydrogen bonds: H:N.99, S:A.39 3PE.12: 33 residues within 4Å: Chain D: R.266 Chain H: W.179, P.180, A.182, M.183, M.184, F.186, I.187, T.238, I.273, Y.277, L.288, N.292, F.293, L.296, L.300, W.303 Chain I: I.60, L.61, M.62, W.63, L.66, I.67, L.70 Chain R: L.43, Y.47 Chain T: E.16, P.17, V.18, V.21, V.25, L.28 Ligands: PC1.13 24 PLIP interactions: 14 interactions with chain H, 5 interactions with chain I, 1 interactions with chain D, 3 interactions with chain T, 1 interactions with chain R Hydrophobic interactions: H:W.179, H:W.179, H:P.180, H:A.182, H:F.186, H:F.186, H:I.187, H:T.238, H:Y.277, H:F.293, H:L.300, H:W.303, H:W.303, I:W.63, I:W.63, I:L.66, I:I.67, I:L.70, T:V.21, T:L.28, R:L.43 Hydrogen bonds: H:N.292, D:R.266, T:E.16

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

NDP.16: 21 residues within 4Å: Chain J: G.60, A.61, 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, V.167, H.169, K.184, P.203, I.206, R.212 19 PLIP interactions: 19 interactions with chain J Hydrophobic interactions: J:P.203, J:I.206, J:I.206 Hydrogen bonds: J:G.60, J:T.62, J:T.62, J:G.63, J:F.64, J:L.65, J:R.85, J:L.129, J:G.131, J:K.184, J:I.206 Salt bridges: J:R.85, J:R.132, J:R.132, J:R.212 pi-Cation interactions: J:R.85

1 x ZN: ZINC ION

ZN.17: 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.18: 15 residues within 4Å: Chain N: S.112, L.113 Chain P: K.32, V.35, W.42, G.62, V.66, M.69, F.70, M.71, N.73, A.74, V.76, V.82, F.110 9 PLIP interactions: 8 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: P:K.32, P:V.35, P:W.42, P:V.66, P:F.70, P:F.110 Hydrogen bonds: P:N.73, N:S.112 Salt bridges: P:K.32

1 x CDL: CARDIOLIPIN

CDL.19: 16 residues within 4Å: Chain H: Y.43 Chain S: M.1, W.2, F.3, P.7 Chain U: L.3, V.6, R.9, G.10, Q.13 Chain V: S.3, A.4, T.5, V.7, I.8, L.11 9 PLIP interactions: 4 interactions with chain V, 3 interactions with chain S, 2 interactions with chain U Hydrophobic interactions: V:V.7, V:I.8, V:L.11, S:W.2, S:F.3, S:P.7, U:L.3 Hydrogen bonds: V:T.5, 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.
Show / Hide

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

Related Entries With Identical Sequence