SMTL ID : 8xnp.1

Respiratory complex Peripheral Arm of CI, close form B, focus-refined map of type IA, Wild type mouse under Cold Acclimation

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(Covalent)

SF4.1: 11 residues within 4Å: Chain B: A.98, C.99, C.100, G.135, 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 SF4.13: 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 SF4.14: 12 residues within 4Å: Chain I: C.113, I.114, A.115, C.116, K.117, C.119, I.130, 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 UQ9: Ubiquinone-9(Non-covalent)

UQ9.2: 18 residues within 4Å: Chain B: F.95, G.96, A.101, M.105, A.108, D.115, V.120, F.121, R.122 Chain D: P.89, H.92, G.93, T.189, D.193, F.200, F.201 Chain H: R.25, R.274 8 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: D:F.200, D:F.201, B:A.101, B:A.108, B:V.120, B:F.121, B:F.121, H:R.25

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

PC1.3: 14 residues within 4Å: Chain B: K.77, D.80, L.81, W.84, R.87, K.213 Chain H: I.39, F.49, M.53 Chain U: F.28, R.29, N.31, W.75, V.77 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:D.80, B:L.81, B:L.81, B:L.81, B:W.84, B:W.84, H:F.49 Salt bridges: B:R.87, B:R.87, B:K.213 PC1.10: 7 residues within 4Å: Chain H: T.66, S.67, M.68, S.69, I.73 Chain J: Y.359 Ligands: 3PE.18 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:I.73 Hydrogen bonds: H:M.68, H:S.69, H:S.69 PC1.12: 19 residues within 4Å: Chain H: W.173, L.175, M.183, L.243, W.272 Chain I: D.55, M.62, T.64, E.65, I.67, R.68, G.71 Chain R: R.28, G.29, L.30, M.35 Chain V: W.14, A.15 Ligands: 3PE.11 9 PLIP interactions: 1 interactions with chain R, 4 interactions with chain H, 2 interactions with chain I, 2 interactions with chain V Salt bridges: R:R.28 Hydrophobic interactions: H:W.173, H:L.243, H:W.272, H:W.272, I:T.64, V:W.14, V:W.14 Hydrogen bonds: I:R.68

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

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 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.134, E:C.139, E:C.175, E:C.179 FES.9: 8 residues within 4Å: Chain G: R.62, F.63, C.64, Y.65, G.73, C.75, 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(Non-covalent)

FMN.5: 20 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, V.242, A.243, N.244, T.247, A.426, L.427 14 PLIP interactions: 14 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:E.209, F:N.244, F:N.244, F:T.247, F:T.247

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

3PE.11: 28 residues within 4Å: Chain D: R.266 Chain H: W.179, P.180, A.182, M.184, F.186, I.187, L.190, P.197, T.238, I.273, Y.277, F.280, L.288, N.292, F.293, L.296, W.303 Chain I: I.60, L.61, W.63, L.66, L.70 Chain T: V.18, V.21, V.25, L.28 Ligands: PC1.12 22 PLIP interactions: 15 interactions with chain H, 2 interactions with chain T, 5 interactions with chain I Hydrophobic interactions: H:W.179, H:W.179, H:A.182, H:F.186, H:F.186, H:F.186, H:I.187, H:L.190, H:P.197, H:T.238, H:I.273, H:Y.277, H:F.293, H:W.303, T:V.25, T:L.28, I:W.63, I:W.63, I:W.63, I:L.66, I:L.70 Hydrogen bonds: H:N.292 3PE.18: 17 residues within 4Å: Chain A: M.1, L.3, Y.4, I.7, F.8, I.11 Chain H: L.81, L.98, N.99, F.104, T.108 Chain R: F.140, T.141, W.142, Y.143 Chain S: A.39 Ligands: PC1.10 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain R, 5 interactions with chain H Hydrophobic interactions: A:L.3, A:Y.4, A:I.7, A:F.8, A:I.11, H:F.104, H:F.104, H:T.108 Hydrogen bonds: R:F.140, H:N.99, H:N.99

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

NDP.15: 24 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, A.110, L.129, I.130, G.131, R.132, E.133, F.139, V.144, V.167, H.169, K.184, P.203, S.204, D.205, I.206 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:P.203, J:I.206 Hydrogen bonds: J:G.60, J:T.62, J:T.62, J:F.64, J:L.65, J:R.85, J:L.129, J:G.131, J:E.133 Salt bridges: J:R.85, J:R.132, J:R.132 pi-Cation interactions: J:R.85

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 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(Non-covalent)

EHZ.17: 15 residues within 4Å: Chain N: S.112 Chain P: L.28, K.32, V.35, W.42, M.69, F.70, M.71, N.73, A.74, V.76, V.82, L.85, F.109, F.110 8 PLIP interactions: 7 interactions with chain P, 1 interactions with chain N Hydrophobic interactions: P:K.32, P:V.35, P:W.42, P:F.109, P:F.110 Hydrogen bonds: P:N.73, N:S.112 Salt bridges: P:K.32

1 x CDL: CARDIOLIPIN(Non-covalent)

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

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

2024-10-30

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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