6DM1

Open state GluA2 in complex with STZ and blocked by NASPM, after micelle signal subtraction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Mechanisms of Channel Block in Calcium-Permeable AMPA Receptors.

Twomey, E.C.Yelshanskaya, M.V.Vassilevski, A.A.Sobolevsky, A.I.

(2018) Neuron 99: 956-968.e4

  • DOI: https://doi.org/10.1016/j.neuron.2018.07.027
  • Primary Citation of Related Structures:  
    6DLZ, 6DM0, 6DM1, 6O9G

  • PubMed Abstract: 

    AMPA receptors mediate fast excitatory neurotransmission and are critical for CNS development and function. Calcium-permeable subsets of AMPA receptors are strongly implicated in acute and chronic neurological disorders. However, despite the clinical importance, the therapeutic landscape for specifically targeting them, and not the calcium-impermeable AMPA receptors, remains largely undeveloped. To address this problem, we used cryo-electron microscopy and electrophysiology to investigate the mechanisms by which small-molecule blockers selectively inhibit ion channel conductance in calcium-permeable AMPA receptors. We determined the structures of calcium-permeable GluA2 AMPA receptor complexes with the auxiliary subunit stargazin bound to channel blockers, including the orb weaver spider toxin AgTx-636, the spider toxin analog NASPM, and the adamantane derivative IEM-1460. Our structures provide insights into the architecture of the blocker binding site and the mechanism of trapping, which are critical for development of small molecules that specifically target calcium-permeable AMPA receptors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY 10032, 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-2 subunit
A, B, C, D
1,031Rattus norvegicusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Gria2Glur2CACNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y698 (Homo sapiens)
Explore Q9Y698 
Go to UniProtKB:  Q9Y698
PHAROS:  Q9Y698
GTEx:  ENSG00000166862 
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y698P19491
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYZ
Query on CYZ

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
M [auth D]
CYCLOTHIAZIDE
C14 H16 Cl N3 O4 S2
BOCUKUHCLICSIY-KSCJFIISSA-N
GYY
Query on GYY

Download Ideal Coordinates CCD File 
K [auth C]N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2-(naphthalen-1-yl)acetamide
C22 H34 N4 O
ZUINPPQIQARTKX-UHFFFAOYSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
L [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CYZ BindingDB:  6DM1 EC50: min: 2240, max: 1.00e+5 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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 Neurological Disorders and Stroke (NIH/NINDS)United StatesNS093838
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS083660
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206573

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-18
    Changes: Other
  • Version 1.5: 2024-10-16
    Changes: Data collection, Database references, Structure summary