9Y94 | pdb_00009y94

Homomeric Glycine Receptor alpha2 with PTX in an Open State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Human GlyR alpha 2 pore dynamics in gating and inhibition.

Klemm, E.Gibbs, E.Stauffer, M.Mohapatra, D.Meyer, C.Chakrapani, S.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2026.02.013
  • Primary Citation Related Structures: 
    9Y7P, 9Y7W, 9Y7X, 9Y7Z, 9Y80, 9Y8Z, 9Y94, 9Y95, 9Y96

  • PubMed Abstract: 

    Glycine receptors (GlyRs) mediate inhibitory neurotransmission in the central nervous system. The GlyRα2 subtype contributes to critical neural circuitry in early neurodevelopment and is also found in adults. GlyRα2 dysfunctions are implicated in neurodevelopmental disorders, including autism, epilepsy, and cognitive delays. GlyRα2 functional properties and pharmacology are distinct from GlyRα1, but the structural basis for these differences remains poorly defined. Here, we report cryo-electron microscopy structures of full-length, human GlyRα2 reconstituted in peptidiscs captured in multiple conformational states. In addition to symmetric resting and desensitized states, we resolved an asymmetric open state, previously observed only in heteromeric GlyRs. This suggests that asymmetry is intrinsic to GlyRα2, independent of β-subunit incorporation. Furthermore, we identified distinct conformations of GlyRα2 with the pore-blocker picrotoxin, providing new insights into allosteric interactions. These findings uncover the structural basis of GlyRα2 function, providing a foundation for understanding its role in development and in GlyRα2-associated disorders.


  • Organizational Affiliation
    • Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106-4970, USA; Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106-4970, USA; Medical Scientist Training Program, Case Western Reserve University, Cleveland, OH 44106-4970, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine receptor subunit alpha-2
A, B, C, D, E
466Homo sapiensMutation(s): 0 
Gene Names: GLRA2
UniProt & NIH Common Fund Data Resources
Find proteins for P23416 (Homo sapiens)
Explore P23416 
Go to UniProtKB:  P23416
PHAROS:  P23416
GTEx:  ENSG00000101958 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23416
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D],
S [auth E],
T [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 
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
R [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 REFINEMENTPHENIX1.20_4459
RECONSTRUCTIONPHENIX1.19.2_4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States1F30HD114399-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R35 GM134896-06
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM152319

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references