6PLR

CryoEM structure of zebra fish alpha-1 glycine receptor bound with glycine in nanodisc, desensitized state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Mechanism of gating and partial agonist action in the glycine receptor.

Yu, J.Zhu, H.Lape, R.Greiner, T.Du, J.Lu, W.Sivilotti, L.Gouaux, E.

(2021) Cell 184: 957-968.e21

  • DOI: 10.1016/j.cell.2021.01.026
  • Primary Citation of Related Structures:  
    6PLO, 6PM0, 6PLQ, 6PM2, 6PLP, 6PM1, 6PLZ, 6PLS, 6PM4, 6PLR, 6PM3, 6PLU, 6PM6, 6PLT, 6PM5, 6PLW, 6PLV, 6PLY, 6PLX

  • PubMed Abstract: 
  • Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists ...

    Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.


    Organizational Affiliation

    Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address: gouauxe@ohsu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycine receptor subunit alphaZ1A, B, C, D, E458Danio rerioMutation(s): 0 
Gene Names: glra1
Membrane Entity: Yes 
UniProt
Find proteins for O93430 (Danio rerio)
Explore O93430 
Go to UniProtKB:  O93430
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, G, H, I, J2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download Ideal Coordinates CCD File 
AA [auth B], CB [auth D], OA [auth C], QB [auth E], T [auth A]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
GLY (Subject of Investigation/LOI)
Query on GLY

Download Ideal Coordinates CCD File 
AB [auth D], MA [auth C], OB [auth E], R [auth A], Y [auth B]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AC [auth E] , BA [auth B] , BB [auth D] , BC [auth E] , CA [auth B] , DA [auth B] , DB [auth D] , EA [auth B] , 
AC [auth E],  BA [auth B],  BB [auth D],  BC [auth E],  CA [auth B],  DA [auth B],  DB [auth D],  EA [auth B],  EB [auth D],  FA [auth B],  FB [auth D],  GA [auth B],  GB [auth D],  HA [auth B],  HB [auth D],  IA [auth B],  IB [auth D],  JA [auth B],  JB [auth D],  K [auth A],  KA [auth B],  KB [auth D],  L [auth A],  LA [auth B],  LB [auth D],  M [auth A],  MB [auth D],  N [auth A],  NA [auth C],  NB [auth D],  O [auth A],  P [auth A],  PA [auth C],  PB [auth E],  Q [auth A],  QA [auth C],  RA [auth C],  RB [auth E],  S [auth A],  SA [auth C],  SB [auth E],  TA [auth C],  TB [auth E],  U [auth A],  UA [auth C],  UB [auth E],  V [auth A],  VA [auth C],  VB [auth E],  W [auth A],  WA [auth C],  WB [auth E],  X [auth A],  XA [auth C],  XB [auth E],  YA [auth C],  YB [auth E],  Z [auth B],  ZA [auth C],  ZB [auth E]
Unknown ligand
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 StatesR01 GM100400

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references