SMTL ID : 8i6v.1

Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 14 residues within 4Å: Chain A: M.42 Chain B: L.46, G.49, L.50, F.65 Chain C: V.41, G.44, G.45, V.48, G.49, F.53 Chain D: S.723, S.727, K.730 8 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:S.727 Salt bridges: D:K.730 Hydrophobic interactions: B:L.46, B:L.46, B:L.50, B:L.50, B:F.65, C:F.53

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain D: V.232, Y.233, A.234 Ligands: PO4.6 No protein-ligand interaction detected (PLIP) PO4.3: 5 residues within 4Å: Chain D: L.225, L.228 Chain E: R.121, L.216, K.217 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.121 PO4.6: 4 residues within 4Å: Chain D: A.234 Chain E: L.222, F.224 Ligands: PO4.2 No protein-ligand interaction detected (PLIP)

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.4: 10 residues within 4Å: Chain E: K.200, Y.241, R.264, R.266, Y.359, R.361, F.456, S.457, K.458 Ligands: MN.5 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Y.241, E:Y.241, E:Y.359, E:Y.359, E:S.457, E:S.457, E:K.458 Water bridges: E:R.266 Salt bridges: E:K.200, E:R.264, E:R.264, E:R.266, E:R.266, E:K.281, E:R.361, E:K.458, E:K.458

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 3 residues within 4Å: Chain E: R.361, E.426 Ligands: 3PO.4 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.426, E:E.426

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit. Embo J. (2023)

Release Date

2023-03-01

Peptides

Vacuolar transporter chaperone complex subunit 1: ABC
Vacuolar transporter chaperone 3 complex subunit 3: D
Vacuolar transporter chaperone complex subunit 4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Vacuolar transporter chaperone complex subunit 1

Vacuolar transporter chaperone 3 complex subunit 3

Vacuolar transporter chaperone complex subunit 4