9Z6W | pdb_00009z6w

The structure of TMD with 4 TARPs from all native AMPA receptor subtypes

PDB DOI: https://doi.org/10.2210/pdb9Z6W/pdb
EM Map EMD-73863: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Mutation(s): Yes

Deposited: 2025-11-14 Released: 2026-02-04
Deposition Author(s): Park, J., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Efficient and rapid isolation of native AMPA receptor complexes for cryo-EM.

Park, J., Gouaux, E.

(2026) Protein Sci 35: e70483-e70483

PubMed: 41578975 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.70483
Primary Citation of Related Structures:
9Z6U, 9Z6V, 9Z6W

PubMed Abstract:
Isolating native ion channels for structural characterization is routinely achieved by extraction from membrane fractions of tissue with prolonged mild detergent treatment. AMPA receptors (AMPARs), glutamatergic receptors that mediate fast excitatory transmission and synaptic plasticity, are coassembled with diverse auxiliary subunits and transiently-interacting partners to finely regulate processes from trafficking to gating kinetics. Previous studies of the composition and architecture of native AMPARs (nAMPARs) isolated from membrane fractions of rodent brain tissue have revealed many different subunit compositions and non-stochastic assemblies of the auxiliary subunits. However, elucidating the molecular architectures of nAMPARs complexed with less populated or transiently bound proteins has proven challenging. Here, we employ strategies for the rapid solubilization and purification of nAMPARs to increase the likelihood of isolating the greatest range of nAMPARs complexes. By utilizing whole brain tissue and reducing solubilization and purification duration, we purify nAMPARs complexed with a wider variety of auxiliary subunits and binding partners in a sufficient quantity and purity for cryo-electron microscopy studies. We resolve previously unreported subunit compositions and conformations that include ones with a half-splayed ATD layer, as well as complexes with four distinct auxiliary subunit arrangements in the TMD layer.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 258.5 kDa
Atom Count: 8,704
Modeled Residue Count: 1,144
Deposited Residue Count: 2,526
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)	A, C	310	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	B, D	310	Mus musculus	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P23819 (Mus musculus) Explore P23819 Go to UniProtKB: P23819
IMPC: MGI:95809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23819
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mix of voltage-dependent calcium channel gamma subunits	E, F	221	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-8 subunit	G, H	422	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q8VHW2 (Mus musculus) Explore Q8VHW2 Go to UniProtKB: Q8VHW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VHW2
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth C]	GA [auth E] HA [auth F] I [auth A] J [auth A] N [auth A] GA [auth E], HA [auth F], I [auth A], J [auth A], N [auth A], U [auth C], V [auth C], Z [auth C]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain GA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth C]
XVD (Subject of Investigation/LOI) Query on XVD Download Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain LA [auth H] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth H] mmCIF format, chain JA [auth G] mmCIF format, chain LA [auth H]	JA [auth G], LA [auth H]	6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol C₁₄ H₈ Cl F₃ N₂ O₂ COBXSLRIXGQVGS-UHFFFAOYSA-N		Interactions Focus chain JA [auth G] Focus chain LA [auth H] Interactions & Density Focus chain JA [auth G] Focus chain LA [auth H]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C], Y [auth C]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain KA [auth H] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth H]	IA [auth G], KA [auth H]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain IA [auth G] Focus chain KA [auth H] Interactions & Density Focus chain IA [auth G] Focus chain KA [auth H]