8VIC | pdb_00008vic

AP-6 bound human TMEM175

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-01-03 Released: 2024-08-14 
  • Deposition Author(s): Oh, S., Hite, R.K.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Selective Inhibitors for the Lysosomal Parkinson's Disease Channel TMEM175.

Oh, S.Lee, J.Choi, H.J.Kim, S.Sapuru, V.Kim, M.Hite, R.K.

(2024) J Am Chem Soc 146: 23230-23239

  • DOI: https://doi.org/10.1021/jacs.4c05623
  • Primary Citation of Related Structures:  
    8VIC, 8VIE

  • PubMed Abstract: 

    TMEM175 is a lysosomal potassium and proton channel that is associated with the development of Parkinson's disease. Advances in understanding the physiological roles of TMEM175 have been hampered by the absence of selective inhibitors, and studies involving genetic perturbations have yielded conflicting results. Here, we report the discovery and characterization of the first reported TMEM175-selective inhibitors, 2-phenylpyridin-4-ylamine (2-PPA), and AP-6. Cryo-EM structures of human TMEM175 bound by 2-PPA and AP-6 reveal that they act as pore blockers, binding at distinct sites in the pore and occluding the ion permeation pathway. Acute inhibition of TMEM175 by 2-PPA or AP-6 increases the level of lysosomal macromolecule catabolism, thereby accelerating macropinocytosis and other digestive processes. These inhibitors may serve as valuable tools to study the roles of TMEM175 in regulating lysosomal function and provide useful templates for future therapeutic development in Parkinson's disease.


  • Organizational Affiliation
    • Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endosomal/lysosomal potassium channel TMEM175
A, B
504Homo sapiensMutation(s): 0 
Gene Names: TMEM175
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSA9 (Homo sapiens)
Explore Q9BSA9 
Go to UniProtKB:  Q9BSA9
PHAROS:  Q9BSA9
GTEx:  ENSG00000127419 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSA9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AA3 (Subject of Investigation/LOI)
Query on A1AA3

Download Ideal Coordinates CCD File 
C [auth A](2P,2'P)-2,2'-(1,3-phenylene)di(pyridin-4-amine)
C16 H14 N4
XLXGLQRJMSGVPH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-3751
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Data collection, Database references, Structure summary