7OCE: Resting state GluA1/A2 AMPA receptor

Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD). Determined by electron microscopy at 3.1 Å resolution. Released 9 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 18,092
Mol. weight: 567.32 kDa
Ligands: E2Q, PC1, CLR
Released: 9 Jun 2021

Explore 7OCE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OCE contains 106 α-helices and 90 β-strands across 8 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.

Chains A and C: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	388-390	3
β-strand	391-394	4	1
β-strand	398	1	2
β-strand	402	1	2
β-strand	403-404	2	3
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	3
α-helix	420-432	13
β-strand	436-438	3	1
β-strand	449	1	4
β-strand	456	1	4
α-helix	459-464	6
β-strand	470-476	7	1
α-helix	479-484	6
β-strand	485-486	2	5
β-strand	492-494	3	1
β-strand	496-501	6	6
α-helix	508-509	2
β-strand	517	1	7
α-helix	519-540	22
α-helix	569-580	12
α-helix	592-625	34
α-helix	632-637	6
β-strand	642-644	3	6
β-strand	646	1	8
α-helix	650-656	7
α-helix	661-669	9
β-strand	679	1	8
α-helix	682-691	10
β-strand	696-701	6	6
α-helix	702-709	8
β-strand	716-719	4	6
β-strand	726-731	6	1
β-strand	732-733	2	5
α-helix	740-752	13
α-helix	754-763	10
β-strand	783	1	9
α-helix	784	1
α-helix	789-819	31

Chain B: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	397-398	2	10
β-strand	407-408	2	11
α-helix	409	1
β-strand	421-422	2	11
α-helix	424-436	13
β-strand	452-453	2	12
β-strand	460-461	2	12
α-helix	462-468	7
β-strand	474-475	2	10
α-helix	479	1
β-strand	480	1	13
α-helix	481	1
α-helix	483-486	4
β-strand	489-491	3	10
β-strand	496-498	3	13
β-strand	500-505	6	14
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	9
α-helix	523-546	24
α-helix	573-584	12
α-helix	596-625	30
α-helix	637-641	5
β-strand	646-648	3	14
β-strand	650	1	15
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	15
α-helix	686-695	10
β-strand	700-705	6	14
α-helix	706-712	7
β-strand	720-723	4	14
β-strand	730-732	3	13
β-strand	735-737	3	10
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	782-786	5
β-strand	787	1	16
α-helix	789-791	3
α-helix	793-821	29

Chain D: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	398	1	18
β-strand	407-408	2	19
α-helix	409	1
β-strand	421-422	2	19
α-helix	424-436	13
β-strand	452-453	2	20
β-strand	460-461	2	20
α-helix	462-468	7
β-strand	475	1	18
α-helix	479	1
β-strand	480	1	21
α-helix	481	1
α-helix	483-486	4
β-strand	489-491	3	18
β-strand	496-498	3	21
β-strand	500-505	6	22
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	23
α-helix	523-546	24
α-helix	573-584	12
α-helix	596-625	30
α-helix	637-641	5
β-strand	646-648	3	22
β-strand	650	1	24
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	24
α-helix	686-695	10
β-strand	700-705	6	22
α-helix	706-712	7
β-strand	720-723	4	22
β-strand	730-732	3	21
β-strand	735-737	3	18
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	782-786	5
β-strand	787	1	7
α-helix	789-791	3
α-helix	793-821	29

Chains E and G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	5-39	35
α-helix	47-66	20
α-helix	68-84	17
α-helix	88-107	20
α-helix	125-158	34

Chains I and J: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	17-40	24
β-strand	45-49	5	17
β-strand	80-84	5	17
β-strand	88-91	4	17
β-strand	100-102	3	17
α-helix	116-127	12
α-helix	129-148	20
α-helix	158-183	26
β-strand	200-201	2	17
α-helix	203-239	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 1	A, C	protein	915	Rattus norvegicus	P19490 (AlphaFold model)
Glutamate receptor 2	B, D	protein	860	Rattus norvegicus	P19491 (AlphaFold model)
Protein cornichon homolog 2	E, G	protein	188	Rattus norvegicus	Q5BJU5 (AlphaFold model)
Voltage-dependent calcium channel gamma-8 subunit	I, J	protein	422	Rattus norvegicus	Q8VHW5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7OCE_1 Glutamate receptor 1 (chains A, C)
MPYIFAFFCTGFLGAVVGADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEP
PKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPS
FPVDTSNQFVLQLRPELQEALISIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQV
TAVNILTTTEEGYRMLFQDLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILAN
LGFMDIDLNKFKESGANVTGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSAL
TYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGN
VQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAATDAQAGGDNSSVQNRTYIVT
TILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTK
AWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL
DPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLW
FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED
LAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKG
KYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGV
LDKLKSKWWYDKGECGSKDSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKS
RSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGGGSGENGRVVSQDFPKSMQSIP
CMSHSSGMPLGATGL

Sequence of entity 2 (B, D), FASTA

>7OCE_2 Glutamate receptor 2 (chains B, D)
MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTP
HIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDG
THPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINV
GNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANL
GFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALT
YDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNI
KFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTT
ILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLD
PLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWF
SLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDL
SKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGK
YAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVL
DKLKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSR
AEAKRMKVAKNPQNINPSSS

Sequence of entity 3 (E, G), FASTA

>7OCE_3 Protein cornichon homolog 2 (chains E, G)
MAFTFAAFCYMLTLVLCASLIFFVIWHIIAFDELRTDFKNPIDQGNPARARERLKNIERI
CCLLRKLVVPEYSIHGLFCLMFLCAAEWVTLGLNIPLLFYHLWRYFHRPADGSEVMYDAV
SIMNADILNYCQKESWCKLAFYLLSFFYYLYSMVYTLVSFENLYFQSGGSTETSQVAPAY
PYDVPDYA

Sequence of entity 4 (I, J), FASTA

>7OCE_4 Voltage-dependent calcium channel gamma-8 subunit (chains I, J)
ESLKRWNEERGLWCEKGVQVLLTTIGAFAAFGLMTIAISTDYWLYTRALICNTTNLTAGD
DGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLL
RVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYIS
ANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSDL
LKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFAS
TDISMYTLSRDPSKGSVAAGLASAGGGGGGAGVGAYGGAAGAAGGGGTGSERDRGSSAGF
LTLHNAFPKEAASGVTVTVTGPPAAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKLEVL
FQ

Ligands and cofactors

ID	Name	Formula	Copies
E2Q	6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide	C12 H8 N4 O6 S	4
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	46
CLR	Cholesterol	C27 H46 O	2

Primary citation

Gating and modulation of a hetero-octameric AMPA glutamate receptor. Zhang, D., Watson, J.F., Matthews, P.M. et al. Nature (2021) 594:454-458. DOI 10.1038/s41586-021-03613-0 · PubMed

Other PDB entries of the same protein (UniProt P19490 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2AWW 2.21 Å, Synapse associated protein 97 PDZ2 domain variant C378G with C-terminal GluR-A peptide
3SAJ 2.5 Å, Crystal Structure of glutamate receptor GluA1 Amino Terminal Domain
8C2H 2.64 Å, Transmembrane domain of active state homomeric GluA1 AMPA receptor in tandem with TARP…
8C2I 2.7 Å, Transmembrane domain of resting state homomeric GluA1 AMPA receptor in complex with TARP…
8AYN 2.8 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481
8C1Q 2.82 Å, Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
8C1P 2.9 Å, Active state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
8AYL 3.2 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059
9OVU 3.2 Å, Composite map of GluA1/A2 in the activated state, in complex with positive allosteric…
9NR6 3.26 Å, The structure of Noelin 1 with cerebellar GluA1/A4-ATD
8AYM 3.3 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118
8AYO 3.3 Å, Open state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059

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