6PEQ | pdb_00006peq

GluA2 in complex with its auxiliary subunit CNIH3 - map LBD-TMD-C3 - with antagonist ZK200775 -without NTD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6PEQ

This is version 1.3 of the entry. See complete history

Literature

Structures of the AMPA receptor in complex with its auxiliary subunit cornichon.

Nakagawa, T.

(2019) Science 366: 1259-1263

  • DOI: https://doi.org/10.1126/science.aay2783
  • Primary Citation Related Structures: 
    6PEQ, 6U5S, 6U6I, 6UCB, 6UD4, 6UD8

  • PubMed Abstract: 

    In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes are critical for synaptic plasticity, learning, and memory. The two major categories of AMPAR auxiliary subunits are transmembrane AMPAR regulatory proteins (TARPs) and cornichon homologs (CNIHs); these subunits share little homology and play distinct roles in controlling ion channel gating and trafficking of AMPAR. Here, I report high-resolution cryo-electron microscopy structures of AMPAR in complex with CNIH3. Contrary to its predicted membrane topology, CNIH3 lacks an extracellular domain and instead contains four membrane-spanning helices. The protein-protein interaction interface that dictates channel modulation and the lipids surrounding the complex are revealed. These structures provide insights into the molecular mechanism for ion channel modulation and assembly of AMPAR/CNIH3 complexes.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biophysics, Center for Structural Biology, and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 488.77 kDa 
  • Atom Count: 16,326 
  • Modeled Residue Count: 2,044 
  • Deposited Residue Count: 4,252 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor 2A,
B,
G [auth C],
H [auth D]
889Rattus norvegicusMutation(s): 0 
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cornichon homolog 3C [auth E],
D [auth F],
E [auth G],
F [auth H]
174Mus musculusMutation(s): 0 
Gene Names: Cnih3
Membrane Entity: Yes 
UniProt
Find proteins for Q6ZWS4 (Mus musculus)
Explore Q6ZWS4 
Go to UniProtKB:  Q6ZWS4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZWS4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZK1
(Subject of Investigation/LOI)

Query on ZK1



Download:Ideal Coordinates CCD File
FA [auth D],
I [auth A],
N [auth B],
Z [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
CLR
(Subject of Investigation/LOI)

Query on CLR



Download:Ideal Coordinates CCD File
T [auth E],
U [auth F],
W [auth G],
X [auth H]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC
(Subject of Investigation/LOI)

Query on OLC



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
GA [auth D]
HA [auth D]
IA [auth D]
AA [auth C],
BA [auth C],
GA [auth D],
HA [auth D],
IA [auth D],
J [auth A],
O [auth B],
P [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
PAM
(Subject of Investigation/LOI)

Query on PAM



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
JA [auth D]
K [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
V [auth F],
Y [auth H]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.06

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2019-12-04 
  • Deposition Author(s): Nakagawa, T.

Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01HD061543

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-18
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary