8AYO | pdb_00008ayo

Open state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8AYO

This is version 2.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 493.52 kDa 
  • Atom Count: 14,512 
  • Modeled Residue Count: 1,958 
  • Deposited Residue Count: 4,396 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 1
A, C
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform Flip of Glutamate receptor 2B [auth D],
F [auth B]
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-8 subunitD [auth I],
E [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
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
(Subject of Investigation/LOI)

Query on POV



Download:Ideal Coordinates CCD File
L [auth A],
U [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
OIJ
(Subject of Investigation/LOI)

Query on OIJ



Download:Ideal Coordinates CCD File
CA [auth J],
W [auth I]
5-[2-(4-fluorophenyl)-7-(4-oxidanylpiperidin-1-yl)pyrazolo[1,5-c]pyrimidin-3-yl]-1,3-dihydroindol-2-one
C25 H22 F N5 O2
UWIJVELUZWBFEU-UHFFFAOYSA-N
CYZ
(Subject of Investigation/LOI)

Query on CYZ



Download:Ideal Coordinates CCD File
EA [auth B],
H [auth A],
N [auth D],
Q [auth C]
CYCLOTHIAZIDE
C14 H16 Cl N3 O4 S2
BOCUKUHCLICSIY-KSCJFIISSA-N
OLC
(Subject of Investigation/LOI)

Query on OLC



Download:Ideal Coordinates CCD File
FA [auth B],
I [auth A],
O [auth D],
R [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
AA [auth J]
BA [auth J]
J [auth A]
K [auth A]
S [auth C]
AA [auth J],
BA [auth J],
J [auth A],
K [auth A],
S [auth C],
T [auth C],
V [auth I],
X [auth I],
Y [auth I],
Z [auth J]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
GLU
(Subject of Investigation/LOI)

Query on GLU



Download:Ideal Coordinates CCD File
DA [auth B],
G [auth A],
M [auth D],
P [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CYZ BindingDB:  8AYO EC50: min: 1000, max: 1.00e+5 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description
  • Version 2.1: 2024-11-13
    Changes: Data collection, Structure summary