9BIS

Cryo-EM structure of the mammalian peptide transporter PepT2 bound to amoxicillin

• PDB DOI: https://doi.org/10.2210/pdb9BIS/pdb
• EM Map EMD-44600: 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)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for antibiotic transport and inhibition in the mammalian proton-coupled peptide transporter, PepT2

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 97.34 kDa 
• Atom Count: 4,710 
• 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 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
AXL (Subject of Investigation/LOI)	C [auth A]	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID C16 H21 N3 O5 S SMLJDSWXGVMNTH-NRWUCQMLSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

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.

---

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