8Y5F | pdb_00008y5f

Cryo-EM structure of E.coli spermidine transporter PotABC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural insights into polyamine spermidine uptake by the ABC transporter PotD-PotABC.

Qiao, Z.Do, P.H.Yeo, J.Y.Ero, R.Li, Z.Zhan, L.Basak, S.Gao, Y.G.

(2024) Sci Adv 10: eado8107-eado8107

  • DOI: https://doi.org/10.1126/sciadv.ado8107
  • Primary Citation Related Structures: 
    8Y5F, 8Y5G, 8Y5H, 8Y5I, 8ZX1

  • PubMed Abstract: 

    Polyamines, characterized by their polycationic nature, are ubiquitously present in all organisms and play numerous cellular functions. Among polyamines, spermidine stands out as the predominant type in both prokaryotic and eukaryotic cells. The PotD-PotABC protein complex in Escherichia coli , belonging to the adenosine triphosphate-binding cassette transporter family, is a spermidine-preferential uptake system. Here, we report structural details of the polyamine uptake system PotD-PotABC in various states. Our analyses reveal distinct "inward-facing" and "outward-facing" conformations of the PotD-PotABC transporter, as well as conformational changes in the "gating" residues (F222, Y223, D226, and K241 in PotB; Y219 and K223 in PotC) controlling spermidine uptake. Therefore, our structural analysis provides insights into how the PotD-PotABC importer recognizes the substrate-binding protein PotD and elucidates molecular insights into the spermidine uptake mechanism of bacteria.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

Macromolecule Content 

  • Total Structure Weight: 147.53 kDa 
  • Atom Count: 9,846 
  • Modeled Residue Count: 1,240 
  • Deposited Residue Count: 1,305 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spermidine/putrescine import ATP-binding protein PotA
A, D
378Escherichia coliMutation(s): 1 
Gene Names: potAb1126JW1112
EC: 7.6.2.11
Membrane Entity: Yes 
UniProt
Find proteins for P69874 (Escherichia coli (strain K12))
Explore P69874 
Go to UniProtKB:  P69874
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69874
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spermidine/putrescine transport system permease protein PotB285Escherichia coliMutation(s): 0 
Gene Names: potBb1125JW1111
Membrane Entity: Yes 
UniProt
Find proteins for P0AFK4 (Escherichia coli (strain K12))
Explore P0AFK4 
Go to UniProtKB:  P0AFK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFK4
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spermidine/putrescine transport system permease protein PotC264Escherichia coliMutation(s): 0 
Gene Names: potCb1124JW1110
Membrane Entity: Yes 
UniProt
Find proteins for P0AFK6 (Escherichia coli (strain K12))
Explore P0AFK6 
Go to UniProtKB:  P0AFK6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFK6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release