6VM2

Full length Glycine receptor reconstituted in lipid nanodisc in Gly/IVM-conformation (State-2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 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

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: 10.1038/s41467-020-17364-5
  • Structures With Same Primary Citation

  • 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 st ...

    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.


    Related Citations: 
    • Glycine receptor mechanism elucidated by electron cryo-microscopy.
      Du, J., Lu, W., Wu, S., Cheng, Y., Gouaux, E.
      (2015) Nature 526: 224

    Organizational Affiliation

    Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. Sudha.chakrapani@case.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine receptor subunit alphaZ1A, B, C, D, E444Danio rerioMutation(s): 0 
Gene Names: glra1
Find proteins for O93430 (Danio rerio)
Explore O93430 
Go to UniProtKB:  O93430
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, H, I, J
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IVM
Query on IVM

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A, B, C, D, E
(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
C48 H74 O14
AZSNMRSAGSSBNP-XPNPUAGNSA-N
 Ligand Interaction
PIO
Query on PIO

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A, B, C, D, E
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
 Ligand Interaction
GLY
Query on GLY

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A, B, C, D, E
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references, Structure summary