9BP7 | pdb_00009bp7

Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP

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

  • Deposited: 2024-05-07 Released: 2025-05-14 
  • Deposition Author(s): Liu, X., Wang, W.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of human alpha 3 beta GlyR regulation by intracellular M3/M4 loop phosphorylation and 2,6-di-tert-butylphenol interaction.

Liu, X.Krezel, M.Wang, W.

(2025) Nat Commun 16: 5242-5242

  • DOI: https://doi.org/10.1038/s41467-025-60516-8
  • Primary Citation of Related Structures:  
    9BOY, 9BOZ, 9BP7

  • PubMed Abstract: 

    α3β glycine receptor (GlyR) is a subtype of GlyRs that belongs to the Cys-loop receptor superfamily. It is highly expressed in the spinal dorsal horn where sensory information is integrated. Under inflammatory conditions, the large unstructured intracellular M3/M4 loops of the α3 subunit are phosphorylated through the prostaglandin E2 (PGE 2 ) pathway, inhibiting ion conduction, and resulting in elevated pain sensation. A small molecule analgesic analog, 2,6-di-tert-butylphenol (2,6-DTBP) potentiates phosphorylated α3β GlyR through unclear mechanisms and relieves pain. Combining cryo-Electron Microscopy (cryo-EM) structures and single molecule Förster resonance energy transfer (smFRET) experiments, we show compaction of M3/M4 loop towards the ion conduction pore upon phosphorylation and further by 2,6-DTBP binding, which in turn modulates function through changing pore conformations and local electrostatics. We show that simultaneous interactions with the M3/M4 loop and the transmembrane domain (TM) is necessary for the potentiation of heteromeric α3β GlyR by 2,6-DTBP, while TM interaction alone is sufficient to potentiate homomeric α3 GlyR, explaining the mystery of why 2,6-DTBP potentiates only phosphorylated α3β GlyR. These findings show how post-translational modification of the unstructured intracellular M3/M4 loop may regulate Cys-loop receptor function, providing new perspectives in pain control and other pharmaceutical development targeting GlyRs and other Cys-loop receptors.


  • Organizational Affiliation
    • Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor subunit alpha-3
A, B, C, D
422Homo sapiensMutation(s): 0 
Gene Names: GLRA3
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens)
Explore O75311 
Go to UniProtKB:  O75311
PHAROS:  O75311
GTEx:  ENSG00000145451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75311
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O75311-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor subunit beta,Green fluorescent protein680Homo sapiensMutation(s): 0 
Gene Names: GLRBMMB69_26960
UniProt & NIH Common Fund Data Resources
Find proteins for P48167 (Homo sapiens)
Explore P48167 
Go to UniProtKB:  P48167
PHAROS:  P48167
GTEx:  ENSG00000109738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48167
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P48167-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
I [auth C],
K [auth D],
L [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLY (Subject of Investigation/LOI)
Query on GLY

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth E]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

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 States1R35GM146860

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references