9VSR | pdb_00009vsr

The DCY1040 and TUG-891-bound structure of TMEM175


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into the activation of TMEM175 by small molecule.

Zhu, X.Ping, M.Liu, H.Yu, T.Jiang, Z.Liu, Z.Li, C.Hou, X.Chu, Q.Li, S.Mao, C.Luo, T.Kang, C.Wang, F.Yang, C.Tang, M.Jiang, Z.Gao, Z.Liu, H.Xu, H.E.Tang, B.Cheng, X.Yin, W.Zhou, Y.Li, P.

(2025) Neuron 

  • DOI: https://doi.org/10.1016/j.neuron.2025.07.029
  • Primary Citation of Related Structures:  
    9VSP, 9VSQ, 9VSR

  • PubMed Abstract: 

    The upregulation of transmembrane protein 175 (TMEM175) has the potential to improve Parkinson's disease (PD) by aiding in the removal of α-synuclein aggregates. Understanding the structural basis of TMEM175 agonisms is crucial for uncovering its therapeutic potential for PD. Here, we have identified the first cryo-electron microscopy (cryo-EM) structure of human TMEM175 complexes with three agonists: DCY1020, DCY1040, and TUG-891. An open state of TMEM175 is unequivocally captured, laying the groundwork for designing more effective agonists. Further investigations using surface plasmon resonance, systematic mutagenesis, whole-endolysosome patch-clamp techniques, and molecular dynamics simulations consistently revealed that DCY1020/1040 binds at the interface between two subunits, inducing an open conformation further augmented by the synergistic agonist TUG-891. Notably, these agonists facilitate the removal of pathological α-synuclein and restore functions of PD-related TMEM175 variants in neurons. Our findings provide proof of concept that drug discovery targeting TMEM175 can develop agonists capable of effectively reducing pathological α-synuclein levels in PD.


  • Organizational Affiliation
    • Zhongshan Institute for Drug Discovery, SIMM, Zhongshan 528400, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endosomal/lysosomal proton 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ETE (Subject of Investigation/LOI)
Query on A1ETE

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
(2S)-2-butyl-2-cyclohexyl-6,7-bis(fluoranyl)-5-[3-(1H-1,2,3,4-tetrazol-5-yl)propoxy]-3H-inden-1-one
C23 H30 F2 N4 O2
DZJNIVKWDLDGEH-QHCPKHFHSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
YN9 (Subject of Investigation/LOI)
Query on YN9

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
3-{4-[(4-fluoro-4'-methyl[1,1'-biphenyl]-2-yl)methoxy]phenyl}propanoic acid
C23 H21 F O3
LPGBXHWIQNZEJB-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release