9ZKT | pdb_00009zkt

The TMD structure of native mouse AMPAR with 2 TARPs 2 CNIHs and PRRT1/SynDIG4

PDB DOI: https://doi.org/10.2210/pdb9ZKT/pdb
EM Map EMD-74384: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2025-12-07 Released: 2026-04-29
Deposition Author(s): Fang, C.L., Gouaux, E.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 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

Native AMPA receptor architecture reveals SynDIG4 engagement and auxiliary subunit heterogeneity

Fang, C.L., Gouaux, E.

To be published.

Macromolecule Content

Total Structure Weight: 378.11 kDa
Atom Count: 9,580
Modeled Residue Count: 1,201
Deposited Residue Count: 3,406
Unique protein chains: 5

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 1	A, C	500	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P23818 (Mus musculus) Explore P23818 Go to UniProtKB: P23818
IMPC: MGI:95808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23818
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	B, D	467	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for C9K0Z0 (Mus musculus) Explore C9K0Z0 Go to UniProtKB: C9K0Z0
IMPC: MGI:95809
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C9K0Z0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cornichon homolog 2	E, F	160	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O35089 (Mus musculus) Explore O35089 Go to UniProtKB: O35089
IMPC: MGI:1277225
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35089
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-8 subunit	G, H	423	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q8VHW2 (Mus musculus) Explore Q8VHW2 Go to UniProtKB: Q8VHW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8VHW2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline-rich transmembrane protein 1	I [auth M]	306	Mus musculus	Mutation(s): 0
UniProt
Find proteins for O35449 (Mus musculus) Explore O35449 Go to UniProtKB: O35449
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35449
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth D] SDF format, chain Z [auth G] MOL2 format, chain L [auth A] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth G] mmCIF format, chain L [auth A] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth G]	L [auth A], X [auth D], Z [auth G]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain L [auth A] Focus chain X [auth D] Focus chain Z [auth G] Interactions & Density Focus chain L [auth A] Focus chain X [auth D] Focus chain Z [auth G]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth D] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth D]	K [auth A] M [auth A] P [auth B] Q [auth B] R [auth C] K [auth A], M [auth A], P [auth B], Q [auth B], R [auth C], T [auth C], U [auth C], W [auth D], Y [auth D]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain K [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth D]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain AA [auth M] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth M] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	AA [auth M] J [auth A] N [auth A] O [auth B] S [auth C] AA [auth M], J [auth A], N [auth A], O [auth B], S [auth C], V [auth D]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain J [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth M] Focus chain J [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D]