SMTL ID : 8ucj.1

CryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x CU: COPPER (II) ION(Non-covalent)

CU.1: 4 residues within 4Å: Chain B: H.243, H.292, H.293 Ligands: HEA.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.243, B:H.292, B:H.293

2 x HEA: HEME-A(Non-covalent)

HEA.2: 23 residues within 4Å: Chain B: F.21, L.25, S.32, S.35, L.38, R.39, A.61, H.64, A.65, M.68, L.72, I.376, F.379, H.380, L.383, L.391, F.392, T.426, F.427, M.430, R.440, R.441, F.470 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.25, B:L.38, B:A.65, B:M.68, B:L.72, B:F.379, B:L.383, B:L.391, B:F.392, B:T.426, B:F.427, B:F.427, B:F.470 Hydrogen bonds: B:R.39, B:W.129, B:R.441 Salt bridges: B:R.440, B:R.441 Metal complexes: B:H.380 HEA.3: 26 residues within 4Å: Chain B: W.129, W.239, H.243, V.246, Y.247, H.292, T.311, A.315, F.323, G.354, L.355, G.357, L.360, S.361, D.366, H.370, V.375, H.378, F.379, V.382, L.383, R.440 Chain C: I.35, P.74, L.78 Ligands: CU.1 20 PLIP interactions: 4 interactions with chain C, 16 interactions with chain B, Hydrophobic interactions: C:I.35, C:I.35, C:P.74, C:L.78, B:V.246, B:T.311, B:A.315, B:F.323, B:L.355, B:L.360, B:V.375, B:F.379, B:F.379, B:F.379, B:L.383 Hydrogen bonds: B:Y.247, B:Y.247 Salt bridges: B:H.370, B:R.440 pi-Cation interactions: B:H.293

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.4: 10 residues within 4Å: Chain B: F.97, A.98, R.99 Chain D: H.15, I.62, W.65, E.72, H.79, F.94 Ligands: PTY.7 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:I.62, D:I.62, D:W.65, D:F.94, D:F.94, D:F.94 Hydrogen bonds: D:H.15, D:E.72, D:E.72, B:A.98, B:R.99 Salt bridges: B:R.99 PTY.5: 10 residues within 4Å: Chain B: F.270 Chain C: F.38, I.42, Y.59, G.63, L.65, I.66, W.70 Chain J: I.13, L.14 9 PLIP interactions: 2 interactions with chain J, 7 interactions with chain C Hydrophobic interactions: J:I.13, C:F.38, C:I.42, C:L.65, C:I.66, C:W.70 Salt bridges: J:K.10 Hydrogen bonds: C:Y.59, C:G.63 PTY.7: 20 residues within 4Å: Chain D: L.59, I.62, F.63, V.66, V.69, V.70, G.73, T.74, L.87, F.91, M.218, V.221, I.225, R.229, H.234, H.239, H.240, L.241, G.242 Ligands: PTY.4 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.59, D:I.62, D:F.63, D:V.66, D:F.91, D:V.221, D:I.225 Hydrogen bonds: D:R.229, D:H.234, D:L.241, D:G.242 Salt bridges: D:R.229, D:H.239 PTY.9: 6 residues within 4Å: Chain B: Y.336, W.417 Chain C: N.52 Chain F: H.62, K.67, F.71 7 PLIP interactions: 5 interactions with chain F, 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: F:K.67, F:F.71, B:Y.336 Hydrogen bonds: F:H.62, C:N.52 Salt bridges: F:H.62, F:H.62

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.6: 7 residues within 4Å: Chain C: Q.108, H.171, C.206, E.208, C.210, H.214, M.217 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.206, C:C.210

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain E: C.112, H.120, C.135, C.138 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.112, E:H.120, E:H.120, E:C.135, E:C.138

1 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.10: 17 residues within 4Å: Chain B: T.210 Chain D: Y.189, T.190, A.192, F.194, T.195, I.196, Y.206, A.207, G.210, L.211 Chain L: T.95, L.96, F.97, W.98, N.99, N.103 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain D Hydrophobic interactions: L:L.96, D:L.211 Hydrogen bonds: L:T.95, L:F.97, D:I.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, J. et al., cryoEM structure of Komagataella pastoris Cytochrome c oxidase (11 subunits) in complex with human VMAT2. To Be Published

Release Date

2024-10-09

Peptides

Synaptic vesicular amine transporter: A
Cytochrome c oxidase subunit 1: B
Cytochrome c oxidase subunit 2: C
Cytochrome c oxidase subunit 3: D
Cytochrome c oxidase subunit 4: E
Cytochrome c oxidase subunit 5: F
Cytochrome c oxidase subunit 6: G
Cytochrome c oxidase subunit 7: H
Cytochrome c oxidase subunit 8: I
Cytochrome c oxidase subunit 9: J
Cytochrome c oxidase subunit 12: K
Cytochrome c oxidase subunit 13: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

C
b

D
c

E
d

F
e

G
f

H
g

I
h

J
i

K
j

L
k

Membrane

We predict this structure to be a membrane protein.
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Synaptic vesicular amine transporter

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4

Cytochrome c oxidase subunit 5

Cytochrome c oxidase subunit 6

Cytochrome c oxidase subunit 7

Cytochrome c oxidase subunit 8

Cytochrome c oxidase subunit 9

Cytochrome c oxidase subunit 12

Cytochrome c oxidase subunit 13

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