8AYN

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Modulatory mechanisms of TARP gamma 8-selective AMPA receptor therapeutics.

Zhang, D.Lape, R.Shaikh, S.A.Kohegyi, B.K.Watson, J.F.Cais, O.Nakagawa, T.Greger, I.H.

(2023) Nat Commun 14: 1659-1659

  • DOI: https://doi.org/10.1038/s41467-023-37259-5
  • Primary Citation of Related Structures:  
    8AYL, 8AYM, 8AYN, 8AYO

  • PubMed Abstract: 

    AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators.


  • Organizational Affiliation

    Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 2A [auth B],
D
860Rattus norvegicusMutation(s): 1 
Gene Names: Gria2Glur2
Membrane Entity: Yes 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-8 subunitB [auth I],
C [auth J]
423Rattus norvegicusMutation(s): 0 
Gene Names: Cacng8
Membrane Entity: Yes 
UniProt
Find proteins for Q8VHW5 (Rattus norvegicus)
Explore Q8VHW5 
Go to UniProtKB:  Q8VHW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VHW5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 1E [auth C],
F [auth A]
915Rattus norvegicusMutation(s): 0 
Gene Names: Gria1Glur1
Membrane Entity: Yes 
UniProt
Find proteins for P19490 (Rattus norvegicus)
Explore P19490 
Go to UniProtKB:  P19490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19490
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth C],
HA [auth A],
J [auth B],
T [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
ZK1 (Subject of Investigation/LOI)
Query on ZK1

Download Ideal Coordinates CCD File 
BA [auth A],
G [auth B],
Q [auth D],
U [auth C]
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
C14 H15 F3 N3 O6 P
WZMQMKNCWDCCMT-UHFFFAOYSA-N
OLR
Query on OLR

Download Ideal Coordinates CCD File 
M [auth I],
P [auth J]
6-[(1~{S})-1-[1-[5-(2-hydroxyethyloxy)pyridin-2-yl]pyrazol-3-yl]ethyl]-3~{H}-1,3-benzothiazol-2-one
C19 H18 N4 O3 S
HLTKOFPQDKJCAN-LBPRGKRZSA-N
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
CA [auth A],
H [auth B],
R [auth D],
V [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
I [auth B]
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
I [auth B],
K [auth I],
L [auth I],
N [auth J],
O [auth J],
S [auth D],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OLR BindingDB:  8AYN IC50: min: 65, max: 8.33e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMRU105174197
Wellcome TrustUnited Kingdom223194/Z/21/Z
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR56/R01MH123474

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release