SMTL ID : 8y5i.1

Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in translocation intermidiate state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: F.27, K.30, V.32, S.52, G.53, C.54, G.55, K.56, T.57, T.58, H.206 Chain D: R.143, Q.147, S.149, G.150, G.151, Q.152 Ligands: MG.2 20 PLIP interactions: 8 interactions with chain D, 12 interactions with chain A Hydrogen bonds: D:R.143, D:R.143, D:H.146, D:S.149, D:G.150, D:G.151, D:Q.152, D:Q.152, A:K.30, A:G.53, A:G.53, A:C.54, A:K.56, A:T.57, A:T.58, A:T.58 Salt bridges: A:K.56, A:K.56, A:H.206 pi-Stacking: A:F.27 ATP.3: 18 residues within 4Å: Chain A: R.143, H.146, Q.147, S.149, Q.152 Chain D: F.27, D.28, K.30, V.32, S.52, G.53, G.55, K.56, T.57, T.58, Q.96, H.206 Ligands: MG.4 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:H.146, A:S.149, A:G.151, A:Q.152, D:D.28, D:K.30, D:G.53, D:G.55, D:K.56, D:T.57, D:T.58 Salt bridges: D:K.56, D:H.206 pi-Stacking: D:F.27, D:F.27

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.57, Q.96, D.172 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain D: Q.96, D.172 Ligands: ATP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, Z. et al., Structural insights into polyamine spermidine uptake by the ABC transporter PotD-PotABC. Sci Adv (2024)

Release Date

2024-10-09

Peptides

Spermidine/putrescine import ATP-binding protein PotA: AD
Spermidine/putrescine transport system permease protein PotB: B
Spermidine/putrescine transport system permease protein PotC: C
Putrescine-binding periplasmic protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Spermidine/putrescine import ATP-binding protein PotA

Spermidine/putrescine transport system permease protein PotB

Spermidine/putrescine transport system permease protein PotC

Putrescine-binding periplasmic protein

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