7LDE

native AMPA receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition.

Yu, J.Rao, P.Clark, S.Mitra, J.Ha, T.Gouaux, E.

(2021) Nature 594: 448-453

  • DOI: https://doi.org/10.1038/s41586-021-03540-0
  • Primary Citation of Related Structures:  
    7LDD, 7LDE, 7LEP

  • PubMed Abstract: 

    AMPA-selective glutamate receptors mediate the transduction of signals between the neuronal circuits of the hippocampus 1 . The trafficking, localization, kinetics and pharmacology of AMPA receptors are tuned by an ensemble of auxiliary protein subunits, which are integral membrane proteins that associate with the receptor to yield bona fide receptor signalling complexes 2 . Thus far, extensive studies of recombinant AMPA receptor-auxiliary subunit complexes using engineered protein constructs have not been able to faithfully elucidate the molecular architecture of hippocampal AMPA receptor complexes. Here we obtain mouse hippocampal, calcium-impermeable AMPA receptor complexes using immunoaffinity purification and use single-molecule fluorescence and cryo-electron microscopy experiments to elucidate three major AMPA receptor-auxiliary subunit complexes. The GluA1-GluA2, GluA1-GluA2-GluA3 and GluA2-GluA3 receptors are the predominant assemblies, with the auxiliary subunits TARP-γ8 and CNIH2-SynDIG4 non-stochastically positioned at the B'/D' and A'/C' positions, respectively. We further demonstrate how the receptor-TARP-γ8 stoichiometry explains the mechanism of and submaximal inhibition by a clinically relevant, brain-region-specific allosteric inhibitor.


  • Organizational Affiliation

    Vollum Institute, Oregon Health & Science University, Portland, OR, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor 1
A, C
907Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P23818 (Mus musculus)
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Go to UniProtKB:  P23818
IMPC:  MGI:95808
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UniProt GroupP23818
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor
B, D
883Mus musculusMutation(s): 1 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P23819 (Mus musculus)
Explore P23819 
Go to UniProtKB:  P23819
IMPC:  MGI:95809
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UniProt GroupP23819
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cornichon homolog 2
E, F
160Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O35089 (Mus musculus)
Explore O35089 
Go to UniProtKB:  O35089
IMPC:  MGI:1277225
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UniProt GroupO35089
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-8 subunit
G, H
423Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8VHW2 (Mus musculus)
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Go to UniProtKB:  Q8VHW2
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UniProt GroupQ8VHW2
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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
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZK1
Query on ZK1

Download Ideal Coordinates CCD File 
BA [auth B],
IA [auth C],
T [auth A],
WA [auth D]
{[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
XVD (Subject of Investigation/LOI)
Query on XVD

Download Ideal Coordinates CCD File 
FB [auth G],
LB [auth H]
6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
C14 H8 Cl F3 N2 O2
COBXSLRIXGQVGS-UHFFFAOYSA-N
R16
Query on R16

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JA [auth C],
U [auth A]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG
Query on NAG

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CA [auth B]
NA [auth C]
OA [auth C]
PA [auth C]
XA [auth D]
CA [auth B],
NA [auth C],
OA [auth C],
PA [auth C],
XA [auth D],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
C14
Query on C14

Download Ideal Coordinates CCD File 
BB [auth F]
EA [auth B]
HB [auth G]
NB [auth H]
SA [auth D]
BB [auth F],
EA [auth B],
HB [auth G],
NB [auth H],
SA [auth D],
ZA [auth E]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12
Query on D12

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DA [auth B]
DB [auth G]
EB [auth G]
IB [auth H]
JB [auth H]
DA [auth B],
DB [auth G],
EB [auth G],
IB [auth H],
JB [auth H],
RA [auth D]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
Query on D10

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AB [auth F]
CB [auth G]
KB [auth H]
MA [auth C]
X [auth A]
AB [auth F],
CB [auth G],
KB [auth H],
MA [auth C],
X [auth A],
YA [auth E]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9
Query on DD9

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FA [auth B],
HA [auth B],
TA [auth D],
VA [auth D]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
OCT
Query on OCT

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GA [auth B]
GB [auth G]
KA [auth C]
MB [auth H]
UA [auth D]
GA [auth B],
GB [auth G],
KA [auth C],
MB [auth H],
UA [auth D],
V [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HP6
Query on HP6

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AA [auth A],
LA [auth C],
QA [auth C],
W [auth A]
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS038631

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references