7LDD | pdb_00007ldd

native AMPA receptor

PDB DOI: https://doi.org/10.2210/pdb7LDD/pdb
EM Map EMD-23283: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli, Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-01-13 Released: 2021-05-12
Deposition Author(s): Yu, J., Rao, P., 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: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 33981040 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-021-03540-0
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 698.54 kDa
Atom Count: 34,528
Modeled Residue Count: 4,990
Deposited Residue Count: 6,234
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 1	A, C	907	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
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
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P23818-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor	B, D	883	Mus musculus	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23819
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D	Go to GlyGen: P23819-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cornichon homolog 2	E, F	160	Mus musculus	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35089
Sequence Annotations Expand
Reference Sequence

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| 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 Membrane Entity: Yes
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

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
11B8 scFv	I, L	257	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab light chain	J, M	225	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab heavy chain	K, N	262	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	2		N-Glycosylation	Interactions Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Interactions & Density Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZK1 Query on ZK1 Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain JA [auth C] SDF format, chain U [auth A] SDF format, chain WA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain WA [auth D]	CA [auth B], JA [auth C], U [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		Interactions Focus chain CA [auth B] Focus chain JA [auth C] Focus chain U [auth A] Focus chain WA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain JA [auth C] Focus chain U [auth A] Focus chain WA [auth D]
XVD (Subject of Investigation/LOI) Query on XVD Download:Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain LB [auth H] MOL2 format, chain FB [auth G] MOL2 format, chain LB [auth H] mmCIF format, chain FB [auth G] mmCIF format, chain LB [auth H]	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		Interactions Focus chain FB [auth G] Focus chain LB [auth H] Interactions & Density Focus chain FB [auth G] Focus chain LB [auth H]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain V [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain V [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain V [auth A]	KA [auth C], V [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain KA [auth C] Focus chain V [auth A] Interactions & Density Focus chain KA [auth C] Focus chain V [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain DA [auth B] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain XA [auth D] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain XA [auth D] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain XA [auth D] mmCIF format, chain Z [auth A]	AA [auth A] DA [auth B] OA [auth C] PA [auth C] XA [auth D] AA [auth A], DA [auth B], OA [auth C], PA [auth C], XA [auth D], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain DA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain DA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain XA [auth D] Focus chain Z [auth A]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain FA [auth B] SDF format, chain HB [auth G] SDF format, chain NB [auth H] SDF format, chain SA [auth D] SDF format, chain ZA [auth E] MOL2 format, chain BB [auth F] MOL2 format, chain FA [auth B] MOL2 format, chain HB [auth G] MOL2 format, chain NB [auth H] MOL2 format, chain SA [auth D] MOL2 format, chain ZA [auth E] mmCIF format, chain BB [auth F] mmCIF format, chain FA [auth B] mmCIF format, chain HB [auth G] mmCIF format, chain NB [auth H] mmCIF format, chain SA [auth D] mmCIF format, chain ZA [auth E]	BB [auth F] FA [auth B] HB [auth G] NB [auth H] SA [auth D] BB [auth F], FA [auth B], HB [auth G], NB [auth H], SA [auth D], ZA [auth E]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain FA [auth B] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain SA [auth D] Focus chain ZA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain FA [auth B] Focus chain HB [auth G] Focus chain NB [auth H] Focus chain SA [auth D] Focus chain ZA [auth E]
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain EB [auth G] SDF format, chain IB [auth H] SDF format, chain JB [auth H] SDF format, chain RA [auth D] SDF format, chain DB [auth G] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth G] MOL2 format, chain IB [auth H] MOL2 format, chain JB [auth H] MOL2 format, chain RA [auth D] MOL2 format, chain DB [auth G] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth G] mmCIF format, chain IB [auth H] mmCIF format, chain JB [auth H] mmCIF format, chain RA [auth D] mmCIF format, chain DB [auth G]	DB [auth G] EA [auth B] EB [auth G] IB [auth H] JB [auth H] DB [auth G], EA [auth B], EB [auth G], IB [auth H], JB [auth H], RA [auth D]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain EA [auth B] Focus chain EB [auth G] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain RA [auth D] Interactions & Density Focus chain DB [auth G] Focus chain EA [auth B] Focus chain EB [auth G] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain RA [auth D]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain CB [auth G] SDF format, chain KB [auth H] SDF format, chain NA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain CB [auth G] MOL2 format, chain KB [auth H] MOL2 format, chain NA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth E] mmCIF format, chain AB [auth F] mmCIF format, chain CB [auth G] mmCIF format, chain KB [auth H] mmCIF format, chain NA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth E]	AB [auth F] CB [auth G] KB [auth H] NA [auth C] Y [auth A] AB [auth F], CB [auth G], KB [auth H], NA [auth C], Y [auth A], YA [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain CB [auth G] Focus chain KB [auth H] Focus chain NA [auth C] Focus chain Y [auth A] Focus chain YA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain CB [auth G] Focus chain KB [auth H] Focus chain NA [auth C] Focus chain Y [auth A] Focus chain YA [auth E]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain TA [auth D] SDF format, chain VA [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain VA [auth D]	GA [auth B], IA [auth B], TA [auth D], VA [auth D]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain IA [auth B] Focus chain TA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain GA [auth B] Focus chain IA [auth B] Focus chain TA [auth D] Focus chain VA [auth D]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain GB [auth G] SDF format, chain HA [auth B] SDF format, chain LA [auth C] SDF format, chain MB [auth H] SDF format, chain UA [auth D] SDF format, chain W [auth A] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MB [auth H] MOL2 format, chain UA [auth D] MOL2 format, chain W [auth A] mmCIF format, chain GB [auth G] mmCIF format, chain HA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MB [auth H] mmCIF format, chain UA [auth D] mmCIF format, chain W [auth A]	GB [auth G] HA [auth B] LA [auth C] MB [auth H] UA [auth D] GB [auth G], HA [auth B], LA [auth C], MB [auth H], UA [auth D], W [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain GB [auth G] Focus chain HA [auth B] Focus chain LA [auth C] Focus chain MB [auth H] Focus chain UA [auth D] Focus chain W [auth A] Interactions & Density Focus chain GB [auth G] Focus chain HA [auth B] Focus chain LA [auth C] Focus chain MB [auth H] Focus chain UA [auth D] Focus chain W [auth A]
HP6 Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain MA [auth C] SDF format, chain QA [auth C] SDF format, chain X [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain X [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain X [auth A]	BA [auth A], MA [auth C], QA [auth C], X [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain MA [auth C] Focus chain QA [auth C] Focus chain X [auth A] Interactions & Density Focus chain BA [auth A] Focus chain MA [auth C] Focus chain QA [auth C] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Yu, J.

Rao, P.

Gouaux, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS038631

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
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Structure summary

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7LDD | pdb_00007ldd

native AMPA receptor

Literature

Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

Entity ID: 6

Entity ID: 7

Oligosaccharides

Entity ID: 8

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)