9BIT

Cryo-EM structure of the mammalian peptide transporter PepT2 bound to cloxacillin, pose 1

• PDB DOI: https://doi.org/10.2210/pdb9BIT/pdb
• EM Map EMD-44601: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Lama glama
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-04-24 Released: 2024-07-24 
• Deposition Author(s): Parker, J.L., Deme, J.C., Lea, S.M., Newstead, S.
• Funding Organization(s): Wellcome Trust, National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for antibiotic transport and inhibition in PepT2.

Parker, J.L., Deme, J.C., Lichtinger, S.M., Kuteyi, G., Biggin, P.C., Lea, S.M., Newstead, S.

(2024) Nat Commun 15: 8755-8755

• PubMed: 39384780 
• DOI: https://doi.org/10.1038/s41467-024-53096-6
• Primary Citation of Related Structures:  
  9BIR, 9BIS, 9BIT, 9BIU


• PubMed Abstract: 
  

  The uptake and elimination of beta-lactam antibiotics in the human body are facilitated by the proton-coupled peptide transporters PepT1 (SLC15A1) and PepT2 (SLC15A2). The mechanism by which SLC15 family transporters recognize and discriminate between different drug classes and dietary peptides remains unclear, hampering efforts to improve antibiotic pharmacokinetics through targeted drug design and delivery. Here, we present cryo-EM structures of the proton-coupled peptide transporter, PepT2 from Rattus norvegicus, in complex with the widely used beta-lactam antibiotics cefadroxil, amoxicillin and cloxacillin. Our structures, combined with pharmacophore mapping, molecular dynamics simulations and biochemical assays, establish the mechanism of beta-lactam antibiotic recognition and the important role of protonation in drug binding and transport.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 97.41 kDa 
• Atom Count: 4,714 
• Modelled Residue Count: 595 
• Deposited Residue Count: 869 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 15 member 2	A	738	Rattus norvegicus	Mutation(s): 0  Gene Names: Slc15a2, Pept2 Membrane Entity: Yes
UniProt
Find proteins for Q63424 (Rattus norvegicus) Explore Q63424  Go to UniProtKB:  Q63424

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	B	131	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXN (Subject of Investigation/LOI)	C [auth A]	CLOXACILLIN C19 H18 Cl N3 O5 S LQOLIRLGBULYKD-JKIFEVAISA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Parker, J.L., Deme, J.C., Lea, S.M., Newstead, S.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	215519
Wellcome Trust	United Kingdom	219531
Wellcome Trust	United Kingdom	218514
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-11-13
  Changes: Data collection