6NJL

Architecture and subunit arrangement of native AMPA receptors


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 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: https://doi.org/10.1126/science.aaw8250
  • Primary Citation of Related Structures:  
    6NJL, 6NJM, 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. 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

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 1
A, C
907Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19490 (Rattus norvegicus)
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Go to UniProtKB:  P19490
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UniProt GroupP19490
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 2
B, D
883Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19491 (Rattus norvegicus)
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Go to UniProtKB:  P19491
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UniProt GroupP19491
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
A'/C' auxiliary proteins
E, G
153Rattus norvegicusMutation(s): 0 
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-2 subunit
F, H
323Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q71RJ2 (Rattus norvegicus)
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UniProt GroupQ71RJ2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
11B8 scFv
I, L
257Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
15F1 Fab light chain
J, M
225Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
15F1 Fab heavy chain
K, N
262Mus musculusMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, P, Q, R, S
O, P, Q, R, S, T
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZK1
Query on ZK1

Download Ideal Coordinates CCD File 
CA [auth D],
U [auth A],
X [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
NAG
Query on NAG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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 1.2: 2020-07-01
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-05-05
    Changes: Structure summary