7BCS

ASCT2 in the presence of the inhibitor Lc-BPE (position "down") in the outward-open conformation.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Rational design of ASCT2 inhibitors using an integrated experimental-computational approach.

Garibsingh, R.A.Ndaru, E.Garaeva, A.A.Shi, Y.Zielewicz, L.Zakrepine, P.Bonomi, M.Slotboom, D.J.Paulino, C.Grewer, C.Schlessinger, A.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2104093118
  • Primary Citation of Related Structures:  
    7BCQ, 7BCS, 7BCT

  • PubMed Abstract: 

    ASCT2 (SLC1A5) is a sodium-dependent neutral amino acid transporter that controls amino acid homeostasis in peripheral tissues. In cancer, ASCT2 is up-regulated where it modulates intracellular glutamine levels, fueling cell proliferation. Nutrient deprivation via ASCT2 inhibition provides a potential strategy for cancer therapy. Here, we rationally designed stereospecific inhibitors exploiting specific subpockets in the substrate binding site using computational modeling and cryo-electron microscopy (cryo-EM). The final structures combined with molecular dynamics simulations reveal multiple pharmacologically relevant conformations in the ASCT2 binding site as well as a previously unknown mechanism of stereospecific inhibition. Furthermore, this integrated analysis guided the design of a series of unique ASCT2 inhibitors. Our results provide a framework for future development of cancer therapeutics targeting nutrient transport via ASCT2, as well as demonstrate the utility of combining computational modeling and cryo-EM for solute carrier ligand discovery.


  • Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutral amino acid transporter B(0)
A, B, C
541Homo sapiensMutation(s): 0 
Gene Names: SLC1A5ASCT2M7V1RDRRDRC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15758 (Homo sapiens)
Explore Q15758 
Go to UniProtKB:  Q15758
PHAROS:  Q15758
GTEx:  ENSG00000105281 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15758
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX1.18.2-3874-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands722.017.001
Netherlands Organisation for Scientific Research (NWO)Netherlands740.018.016
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108911
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesT32 CA078207
National Science Foundation (NSF, United States)United States1515028
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR15 GM135843-01
Netherlands Organisation for Scientific Research (NWO)Netherlands714.018.003

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references, Refinement description