Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.02 kDa 
• Atom Count: 3146 
• Residue Count: 378 
• Unique protein chains: 1

5A9D

Crystal structure of the extracellular domain of PepT1

• DOI: 10.2210/pdb5A9D/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-20 Released: 2015-09-09 
• Deposition Author(s): Beale, J.H., Bird, L.E., Owens, R.J., Newstead, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.238 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Crystal Structures of the Extracellular Domain from Pept1 and Pept2 Provide Novel Insights Into Mammalian Peptide Transport

Beale, J.H., Parker, J.L., Samsudin, F., Barrett, A.L., Senan, A., Bird, L.E., Scott, D., Owens, R.J., Sanson, M.S.P., Tucker, S.J., Meredith, D., Fowler, P.W., Newstead, S.

(2015) Structure 23: 1889

• PubMed: 26320580 
• DOI: 10.1016/j.str.2015.07.016
• Primary Citation of Related Structures:  
  5A9H, 5A9I, 5A9D


• PubMed Abstract: 
  

Mammals obtain nitrogen via the uptake of di- and tri-peptides in the gastrointestinal tract through the action of PepT1 and PepT2, which are members of the POT family of proton-coupled oligopeptide transporters. PepT1 and PepT2 also play an important role in drug transport in the human body. Recent crystal structures of bacterial homologs revealed a conserved peptide-binding site and mechanism of transport. However, a key structural difference exists between bacterial and mammalian homologs with only the latter containing a large extracellular domain, the function of which is currently unknown. Here, we present the crystal structure of the extracellular domain from both PepT1 and PepT2 that reveal two immunoglobulin-like folds connected in tandem, providing structural insight into mammalian peptide transport. Functional and biophysical studies demonstrate that these domains interact with the intestinal protease trypsin, suggesting a role in clustering proteolytic activity to the site of peptide transport in eukaryotic cells.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Membrane Transport, University of Oxford OX1 3PU, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOLUTE CARRIER FAMILY 15 MEMBER 1	A, B	189	Mus musculus	Mutation(s): 0  Gene Names: Slc15a1, Pept1
Find proteins for Q9JIP7 (Mus musculus) Explore Q9JIP7  Go to UniProtKB:  Q9JIP7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.238 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.48	α = 90
b = 70.33	β = 90
c = 111.22	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-20 
• Released Date: 2015-09-09 
Deposition Author(s): Beale, J.H., Bird, L.E., Owens, R.J., Newstead, S.

Revision History 

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Database references
• Version 1.2: 2019-04-03
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation