9PVM | pdb_00009pvm

cryoEM structure of drug bound human SLC33A1 transporter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9PVM

This is version 1.0 of the entry. See complete history

Literature

Pharmacological Inhibition of SLC33A1 Promotes Endoplasmic Reticulum Hyperoxidation and Induces Adaptive IRE1/XBP1s Signaling.

Kutseikin, S.Rafiq, M.Bora, P.Liu, S.Homan, R.A.Mindrebo, J.T.Holcomb, M.Petrassi, H.M.Qiu, H.Redkina, A.Sosna, J.Lee, T.T.Hu, X.Forli, S.Parker, C.G.Lander, G.C.Birsoy, K.Saez, E.Wiseman, R.L.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.02.17.706344
  • Primary Citation Related Structures: 
    9PVM, 9Z5I

  • PubMed Abstract: 

    The endoplasmic reticulum (ER) transporter solute carrier family 33 member 1 (SLC33A1) has emerged as an attractive therapeutic target in etiologically diverse diseases, ranging from lung cancer to neurodegenerative disorders. Yet, no pharmacologic SLC33A1 modulators have been described. Here, we show that the small molecule IXA4, a highly selective activator of the adaptive IRE1/XBP1s signaling arm of the unfolded protein response (UPR), binds to SLC33A1 and inhibits its activity. Genetic depletion of SLC33A1 phenocopies the selective induction of IRE1/XBP1s signaling brought about by IXA4 treatment. Chemoproteomic analyses and cryo-electron microscopy show that IXA4 binds SLC33A1 within the central channel to inhibit transport of its substrate metabolite(s). Binding of IXA4 to SLC33A1 leads to the accumulation of oxidized glutathione within the ER, hyperoxidizing the ER lumen and inducing activation of adaptive IRE1/XBP1s signaling. Consistent with this function, we find that pharmacologic inhibition of SLC33A1 with IXA4 selectively reduces viability of KEAP1-deficient lung adenocarcinoma cells that have elevated levels of glutathione, mimicking the sensitivity of these cells to genetic deletion of SLC33A1. Our work demonstrates a new physiologic role of SLC33A1 in regulation of ER redox homeostasis and designates IXA4 as a pharmacologic inhibitor of SLC33A1 that can be used to evaluate the biological impact and therapeutic utility of SLC33A1 inhibition in homeostasis and in disease.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, The Scripps Research Institute, La Jolla, CA.

Macromolecule Content 

  • Total Structure Weight: 65.79 kDa 
  • Atom Count: 3,596 
  • Modeled Residue Count: 441 
  • Deposited Residue Count: 580 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A transporter 1580Homo sapiensMutation(s): 0 
Gene Names: SLC33A1ACATNAT1
UniProt & NIH Common Fund Data Resources
Find proteins for O00400 (Homo sapiens)
Explore O00400 
Go to UniProtKB:  O00400
GTEx:  ENSG00000169359 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00400
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
A1CTY(
Subject of Investigation/LOI)

Query on A1CTY



Download:Ideal Coordinates CCD File
B [auth A]N-[1-(2-{methyl[2-(4-methylphenoxy)ethyl]amino}-2-oxoethyl)-1H-pyrazol-4-yl]-3-phenoxypropanamide
C24 H28 N4 O4
ZVSKMVAWWBSNOY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7.0
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG046495

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release