6UCB

GluA2 in complex with its auxiliary subunit CNIH3 - with antagonist ZK200775, LBD, TMD, CNIH3, and lipids


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1126/science.aay2783
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2A,
B,
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein cornichon homolog 3D [auth E],
E [auth F],
F [auth G],
G [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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZK1 (Subject of Investigation/LOI)
Query on ZK1

Download Ideal Coordinates CCD File 
GA [auth D],
I [auth A],
M [auth B],
T [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
 Ligand Interaction
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
CA [auth G],
FA [auth H],
S [auth B],
Y [auth E]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

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

Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth G],
DA [auth H],
EA [auth H],
K [auth A],
AA [auth F],
BA [auth G],
DA [auth H],
EA [auth H],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
Q [auth B],
R [auth B],
V [auth C],
W [auth C],
X [auth E],
Z [auth F]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-09-15 
  • 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