Crystal structure of tetrameric PepTSo2 in P4212 space group

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 

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Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2.

Nagamura, R.Fukuda, M.Kawamoto, A.Matoba, K.Dohmae, N.Ishitani, R.Takagi, J.Nureki, O.

(2019) Acta Crystallogr F Struct Biol Commun 75: 348-358

  • DOI: https://doi.org/10.1107/S2053230X19003546
  • Primary Citation of Related Structures:  
    6JI1, 6JKC, 6JKD

  • PubMed Abstract: 

    Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. The human POTs PepT1 and PepT2 are also involved in the absorption of various orally ingested drugs. Previously reported structures revealed that the bacterial POTs possess 14 helices, of which H1-H6 and H7-H12 constitute the typical MFS fold and the residual two helices are involved in the cytoplasmic linker. PepT So2 from Shewanella oneidensis is a unique POT which reportedly assembles as a 200 kDa tetramer. Although the previously reported structures suggested the importance of H12 for tetramer formation, the structural basis for the PepT So2 -specific oligomerization remains unclear owing to the lack of a high-resolution tetrameric structure. In this study, the expression and purification conditions for tetrameric PepT So2 were optimized. A single-particle cryo-EM analysis revealed the tetrameric structure of PepT So2 incorporated into Salipro nanoparticles at 4.1 Å resolution. Furthermore, a combination of lipidic cubic phase (LCP) crystallization and an automated data-processing system for multiple microcrystals enabled crystal structures of PepT So2 to be determined at resolutions of 3.5 and 3.9 Å. The present structures in a lipid bilayer revealed the detailed mechanism for the tetrameric assembly of PepT So2 , in which a characteristic extracellular loop (ECL) interacts with two asparagine residues on H12 which were reported to be important for tetramerization and plays an essential role in oligomeric assembly. This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton:oligopeptide symporter POT family527Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1277
Membrane Entity: Yes 
Find proteins for Q8EHE6 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EHE6 
Go to UniProtKB:  Q8EHE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EHE6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.41α = 90
b = 119.41β = 90
c = 104.31γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan24227004
Japan Society for the Promotion of ScienceJapan25291011

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description