9J8B | pdb_00009j8b

Human Glycine Transporter 1 in the Apo State with an Inward-Facing Conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Modulation of the human GlyT1 by clinical drugs and cholesterol.

Li, N.Wei, Y.Li, R.Meng, Y.Zhao, J.Bai, Q.Wang, G.Zhao, Y.

(2025) Nat Commun 16: 2412-2412

  • DOI: https://doi.org/10.1038/s41467-025-57613-z
  • Primary Citation of Related Structures:  
    9J8B, 9J8C, 9J8D

  • PubMed Abstract: 

    Glycine transporter 1 (GlyT1) is a key player in shaping extracellular glutamatergic signaling processes and holds promise for treating cognitive impairments associated with schizophrenia by inhibiting its activity and thus enhancing the function of NMDA receptors. Despite its significant role in physiological and pharmacology, its modulation mechanism by clinical drugs and internal lipids remains elusive. Here, we determine cryo-EM structures of GlyT1 in its apo state and in complex with clinical trial drugs iclepertin and sarcosine. The GlyT1 in its apo state is determined in three distinct conformations, exhibiting a conformational equilibrium of the transport cycle. The complex structures with inhibitor iclepertin and sarcosine elucidate their unique binding poses with GlyT1. Three binding sites of cholesterol are determined in GlyT1, two of which are conformation-dependent. Transport kinetics studies reveal that a delicate binding equilibrium for cholesterol is crucial for the conformational transition of GlyT1. This study significantly enhances our understanding of the physiological and pharmacological aspects of GlyT1.


  • Organizational Affiliation

    Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1652Homo sapiensMutation(s): 0 
Gene Names: SLC6A9
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48067 (Homo sapiens)
Explore P48067 
Go to UniProtKB:  P48067
PHAROS:  P48067
GTEx:  ENSG00000196517 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48067
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92157102

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-26
    Changes: Data collection, Database references