6NJN

structure of a complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.

Zhao, Y.Chen, S.Swensen, A.C.Qian, W.J.Gouaux, E.

(2019) Science 364: 355-362

  • DOI: 10.1126/science.aaw8250
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite d ...

    Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.


    Organizational Affiliation

    Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. gouauxe@ohsu.edu.,Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 1
A
907Rattus norvegicusMutation(s): 0 
Gene Names: Gria1 (Glur1)
Find proteins for P19490 (Rattus norvegicus)
Go to UniProtKB:  P19490
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
B, D
883Rattus norvegicusMutation(s): 0 
Gene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 3
C
888Rattus norvegicusMutation(s): 0 
Gene Names: Gria3 (Glur3)
Find proteins for P19492 (Rattus norvegicus)
Go to UniProtKB:  P19492
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
A'-C' auxiliary proteins
E, G
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Voltage-dependent calcium channel gamma-2 subunit
F, H
323Rattus norvegicusMutation(s): 0 
Gene Names: Cacng2 (Stg)
Find proteins for Q71RJ2 (Rattus norvegicus)
Go to UniProtKB:  Q71RJ2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
11B8 scFv
I
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
15F1 Fab light chain
J, N
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
15F1 Fab heavy chain
K, O
262N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
5B2 Fab
L, M
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZK1
Query on ZK1

Download SDF File 
Download CCD File 
A, B, C, D
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
[[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid
C14 H15 F3 N3 O6 P
WZMQMKNCWDCCMT-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E, G, L, M
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-01-03 
  • Released Date: 2019-04-24 
  • Deposition Author(s): Gouaux, E., Zhao, Y.

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references