8SS6

Structure of AMPA receptor GluA2 complex with auxiliary subunits TARP gamma-5 and cornichon-2 bound to competitive antagonist ZK, channel blocker spermidine and antiepileptic drug perampanel (closed state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Modulation of GluA2-gamma 5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2.

Gangwar, S.P.Yen, L.Y.Yelshanskaya, M.V.Korman, A.Jones, D.R.Sobolevsky, A.I.

(2023) Nat Struct Mol Biol 30: 1481-1494

  • DOI: https://doi.org/10.1038/s41594-023-01080-x
  • Primary Citation of Related Structures:  
    8BHF, 8SS2, 8SS3, 8SS4, 8SS5, 8SS6, 8SS7, 8SS8, 8SS9, 8SSA, 8SSB

  • PubMed Abstract: 

    Synaptic complexes of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPARs) with auxiliary subunits mediate most excitatory neurotransmission and can be targeted to treat neuropsychiatric and neurological disorders, including epilepsy. Here we present cryogenic-electron microscopy structures of rat GluA2 AMPAR complexes with inhibitory mouse γ5 and potentiating human cornichon-2 (CNIH2) auxiliary subunits. CNIH2 appears to destabilize the desensitized state of the complex by reducing the separation of the upper lobes in ligand-binding domain dimers. At the same time, CNIH2 stabilizes binding of polyamine spermidine to the selectivity filter of the closed ion channel. Nevertheless, CNIH2, and to a lesser extent γ5, attenuate polyamine block of the open channel and reduce the potency of the antiepileptic drug perampanel that inhibits the synaptic complex allosterically by binding to sites in the ion channel extracellular collar. These findings illustrate the fine-tuning of synaptic complex structure and function in an auxiliary subunit-dependent manner, which is critical for the study of brain region-specific neurotransmission and design of therapeutics for disease treatment.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera
A, B, C, D
1,026Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2Cacng5
Membrane Entity: Yes 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Find proteins for Q8VHW8 (Rattus norvegicus)
Explore Q8VHW8 
Go to UniProtKB:  Q8VHW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8VHW8P19491
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cornichon homolog 2
E, F
160Homo sapiensMutation(s): 0 
Gene Names: CNIH2CNIL
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PI25 (Homo sapiens)
Explore Q6PI25 
Go to UniProtKB:  Q6PI25
PHAROS:  Q6PI25
GTEx:  ENSG00000174871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PI25
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
I [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
LA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
QA [auth D],
RA [auth D],
T [auth B],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
XA [auth F],
YA [auth F],
Z [auth B],
ZA [auth F]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
ZK1 (Subject of Investigation/LOI)
Query on ZK1

Download Ideal Coordinates CCD File 
BA [auth C],
H [auth A],
NA [auth D],
S [auth B]
{[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
CLR
Query on CLR

Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
M [auth A]
N [auth A]
SA [auth D]
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
SA [auth D],
TA [auth D],
X [auth B],
Y [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
6ZP (Subject of Investigation/LOI)
Query on 6ZP

Download Ideal Coordinates CCD File 
AA [auth C],
G [auth A],
MA [auth D],
R [auth B]
2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile
C23 H15 N3 O
PRMWGUBFXWROHD-UHFFFAOYSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

Download Ideal Coordinates CCD File 
KA [auth C]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
Q [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.0.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS107253
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesAR078814
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206573

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary