6NJN

Architecture and subunit arrangement of native AMPA receptors


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 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:  
    6NJM, 6NJL, 6NJN

  • 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 decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown ...

    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

    Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 1A907Rattus norvegicusMutation(s): 0 
Gene Names: Gria1Glur1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
Glutamate receptor (AMPA-subtype), GluA1/GluA2/GluA1/GluA2 tetramer
Find proteins for P19490 (Rattus norvegicus)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 2B, D883Rattus norvegicusMutation(s): 0 
Gene Names: Gria2Glur2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
Glutamate receptor (AMPA-subtype), GluA1/GluA2/GluA1/GluA2 tetramer
Find proteins for P19491 (Rattus norvegicus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor 3C888Rattus norvegicusMutation(s): 0 
Gene Names: Gria3Glur3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
Glutamate receptor (AMPA-subtype), GluA1/GluA2/GluA1/GluA2 tetramer
Find proteins for P19492 (Rattus norvegicus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
A'-C' auxiliary proteinsE, G153Rattus norvegicusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-2 subunitF, H323Rattus norvegicusMutation(s): 0 
Gene Names: Cacng2Stg
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
Glutamate receptor (AMPA-subtype), GluA1/GluA2/GluA1/GluA2 tetramer
Find proteins for Q71RJ2 (Rattus norvegicus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
11B8 scFvI257Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
15F1 Fab light chainJ, N225Mus musculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
15F1 Fab heavy chainK, O262Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
5B2 FabL, M224Rattus norvegicusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP, Q, T, U, V3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR, S, W2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZK1
Query on ZK1

Download Ideal Coordinates CCD File 
BA [auth C], CA [auth D], X [auth A], Z [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
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B], DA [auth D], Y [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-05-05
    Changes: Structure summary