8AYL: Resting state GluA1/A2 AMPA receptor

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059. Determined by electron microscopy at 3.2 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 15,702
Mol. weight: 495.53 kDa
Ligands: OIJ, POV, PLM, OLC
Released: 19 Apr 2023

Explore 8AYL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AYL contains 88 α-helices and 98 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	390-391	2	13
β-strand	393-394	2	14
β-strand	403-404	2	15
α-helix	413-416	4
β-strand	417-418	2	15
α-helix	420-432	13
β-strand	435-436	2	13
β-strand	449-450	2	16
β-strand	455-456	2	16
α-helix	459-464	6
β-strand	470-471	2	14
β-strand	476	1	17
α-helix	479-484	6
β-strand	485-487	3	14
α-helix	488-490	3
β-strand	492-494	3	17
β-strand	496-501	6	18
α-helix	512-514	3
β-strand	517	1	19
α-helix	519-540	22
α-helix	569-580	12
α-helix	592-625	34
α-helix	633-637	5
β-strand	642-644	3	18
β-strand	646	1	20
α-helix	650-656	7
α-helix	661-671	11
β-strand	679	1	20
α-helix	682-692	11
β-strand	696-701	6	18
α-helix	702-709	8
β-strand	716-718	3	18
β-strand	726-728	3	17
β-strand	731-733	3	14
α-helix	739-751	13
α-helix	754-760	7
α-helix	761-765	5
β-strand	783	1	7
α-helix	789-811	23

Chains B and D: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	396-399	4	1
β-strand	407-408	2	2
β-strand	421-422	2	2
α-helix	424-436	13
β-strand	441-444	4	1
α-helix	450	1
β-strand	453-454	2	3
β-strand	459-460	2	3
α-helix	463-469	7
β-strand	474-475	2	1
β-strand	480	1	4
α-helix	483-486	4
β-strand	489-491	3	1
β-strand	496-498	3	4
β-strand	500	1	5
β-strand	503-505	3	6
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	7
α-helix	523-545	23
α-helix	573-584	12
α-helix	596-625	30
α-helix	637-641	5
β-strand	646	1	8
β-strand	650	1	9
α-helix	654-661	8
α-helix	665-675	11
β-strand	683	1	9
α-helix	686-696	11
β-strand	700	1	8
β-strand	702	1	6
β-strand	705	1	5
α-helix	706-713	8
β-strand	720-722	3	6
β-strand	730-732	3	4
β-strand	735-737	3	1
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	782-786	5
β-strand	787	1	10
α-helix	793-818	26

Chain C: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	390-391	2	30
β-strand	393-394	2	31
β-strand	403-404	2	32
α-helix	413-416	4
β-strand	417-418	2	32
α-helix	420-432	13
β-strand	435-436	2	30
β-strand	449-450	2	33
β-strand	455-456	2	33
α-helix	459-464	6
β-strand	470-471	2	31
β-strand	476	1	34
α-helix	479-484	6
β-strand	485-487	3	31
α-helix	488-490	3
β-strand	492-494	3	34
β-strand	496	1	35
β-strand	499-501	3	36
α-helix	512-514	3
β-strand	517	1	10
α-helix	519-540	22
α-helix	569-580	12
α-helix	592-625	34
α-helix	633-637	5
β-strand	642-644	3	36
β-strand	646	1	37
α-helix	650-656	7
α-helix	661-671	11
β-strand	679	1	37
α-helix	682-692	11
β-strand	696-698	3	36
β-strand	701	1	35
α-helix	702-709	8
β-strand	716-718	3	36
β-strand	726-728	3	34
β-strand	731-733	3	31
α-helix	739-751	13
α-helix	754-760	7
α-helix	761-765	5
β-strand	783	1	27
α-helix	789-811	23

Chains I and J: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	18-39	22
β-strand	45-48	4	12
β-strand	81-84	4	12
β-strand	91	1	12
α-helix	94-96	3
α-helix	117-127	11
α-helix	129-148	20
α-helix	156-182	27
β-strand	200-201	2	12
α-helix	203-232	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 2	B, D	protein	860	Rattus norvegicus	P19491 (AlphaFold model)
Voltage-dependent calcium channel gamma-8 subunit	I, J	protein	423	Rattus norvegicus	Q8VHW5 (AlphaFold model)
Isoform Flip of Glutamate receptor 1	A, C	protein	915	Rattus norvegicus	P19490 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>8AYL_1 Isoform Flip of Glutamate receptor 2 (chains B, D)
MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTP
HIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDG
THPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINV
GNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANL
GFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALT
YDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNI
KFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTT
ILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLD
PLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWF
SLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDL
SKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGK
YAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVL
DKLKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSR
AEAKRMKVAKNPQNINPSSS

Sequence of entity 2 (I, J), FASTA

>8AYL_2 Voltage-dependent calcium channel gamma-8 subunit (chains I, J)
GESLKRWNEERGLWCEKGVQVLLTTIGAFAAFGLMTIAISTDYWLYTRALICNTTNLTAG
DDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYL
LRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYI
SANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSD
LLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFA
STDISMYTLSRDPSKGSVAAGLASAGGGGGGAGVGAYGGAAGAAGGGGTGSERDRGSSAG
FLTLHNAFPKEAASGVTVTVTGPPAAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKLEV
LFQ

Sequence of entity 3 (A, C), FASTA

>8AYL_3 Isoform Flip of Glutamate receptor 1 (chains A, C)
MPYIFAFFCTGFLGAVVGADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEP
PKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPS
FPVDTSNQFVLQLRPELQEALISIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQV
TAVNILTTTEEGYRMLFQDLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILAN
LGFMDIDLNKFKESGANVTGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSAL
TYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGN
VQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAATDAQAGGDNSSVQNRTYIVT
TILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTK
AWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL
DPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLW
FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED
LAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKG
KYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGV
LDKLKSKWWYDKGECGSKDSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKS
RSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGGGSGENGRVVSQDFPKSMQSIP
CMSHSSGMPLGATGL

Ligands and cofactors

ID	Name	Formula	Copies
OIJ	5-[2-(4-fluorophenyl)-7-(4-oxidanylpiperidin-1-yl)pyrazolo[1,5-c]pyrimidin-3-yl…	C25 H22 F N5 O2	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	6
PLM	Palmitic acid	C16 H32 O2	8
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4
ZK1	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl…	C14 H15 F3 N3 O6 P	4

Primary citation

Modulatory mechanisms of TARP gamma 8-selective AMPA receptor therapeutics. Zhang, D., Lape, R., Shaikh, S.A. et al. Nat Commun (2023) 14:1659-1659. DOI 10.1038/s41467-023-37259-5 · PubMed

Other PDB entries of the same protein (UniProt P19491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YK4 1.0 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5NG9 1.15 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
6YK5 1.15 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
6YK3 1.2 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5JEI 1.23 Å, Crystal structure of the GluA2 LBD in complex with FW
4IGT 1.24 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist…
4YU0 1.26 Å, Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with…
5NIH 1.3 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
1MQI 1.35 Å, Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with…
5FTI 1.35 Å, Crystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
4U21 1.39 Å, GluA2flip sLBD complexed with FW and (R,R)-2b crystal form E
4FAT 1.4 Å, Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an…

Browse structure collections

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