6UD3

Full length Glycine receptor reconstituted in lipid nanodisc in Gly/PTX-bound open/blocked conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs.

Kumar, A.Basak, S.Rao, S.Gicheru, Y.Mayer, M.L.Sansom, M.S.P.Chakrapani, S.

(2020) Nat Commun 11: 3752-3752

  • DOI: https://doi.org/10.1038/s41467-020-17364-5
  • Primary Citation of Related Structures:  
    6UBS, 6UBT, 6UD3, 6VM0, 6VM2, 6VM3

  • PubMed Abstract: 

    Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.


  • Organizational Affiliation

    Department of Physiology and Biophysics, 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 alphaZ1A,
B [auth C],
C [auth E],
D,
E [auth B]
459Danio rerioMutation(s): 0 
Gene Names: glra1
Membrane Entity: Yes 
UniProt
Find proteins for O93430 (Danio rerio)
Explore O93430 
Go to UniProtKB:  O93430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93430
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RI5 (Subject of Investigation/LOI)
Query on RI5

Download Ideal Coordinates CCD File 
H [auth A](1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione
C15 H16 O6
PIMZUZSSNYHVCU-YKWPQBAZSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
K [auth E],
N [auth D],
P [auth B]
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],
L [auth E],
M [auth D],
O [auth B]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM108921-05
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM131216-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references, Structure summary
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references