6ZPL

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the inhibition of glycine reuptake.

Shahsavar, A.Stohler, P.Bourenkov, G.Zimmermann, I.Siegrist, M.Guba, W.Pinard, E.Sinning, S.Seeger, M.A.Schneider, T.R.Dawson, R.J.P.Nissen, P.

(2021) Nature 591: 677-681

  • DOI: https://doi.org/10.1038/s41586-021-03274-z
  • Primary Citation of Related Structures:  
    6ZBV, 6ZPL

  • PubMed Abstract: 

    The human glycine transporter 1 (GlyT1) regulates glycine-mediated neuronal excitation and inhibition through the sodium- and chloride-dependent reuptake of glycine 1-3 . Inhibition of GlyT1 prolongs neurotransmitter signalling, and has long been a key strategy in the development of therapies for a broad range of disorders of the central nervous system, including schizophrenia and cognitive impairments 4 . Here, using a synthetic single-domain antibody (sybody) and serial synchrotron crystallography, we have determined the structure of GlyT1 in complex with a benzoylpiperazine chemotype inhibitor at 3.4 Å resolution. We find that the inhibitor locks GlyT1 in an inward-open conformation and binds at the intracellular gate of the release pathway, overlapping with the glycine-release site. The inhibitor is likely to reach GlyT1 from the cytoplasmic leaflet of the plasma membrane. Our results define the mechanism of inhibition and enable the rational design of new, clinically efficacious GlyT1 inhibitors.


  • Organizational Affiliation

    Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium- and chloride-dependent glycine transporter 1A [auth B],
B [auth A]
576Homo sapiensMutation(s): 4 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endoglucanase H273Acetivibrio thermocellus ATCC 27405Mutation(s): 1 
Gene Names: celHCthe_1472
EC: 3.2.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P16218 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore P16218 
Go to UniProtKB:  P16218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16218
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sybody Sb_GlyT1#7D [auth E],
E [auth F]
120unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.277 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.41α = 90
b = 69.71β = 92.86
c = 149.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmark--
LundbeckfondenDenmark--
F. Hoffmann-La Roche LTDSwitzerland--
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermany664726

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description