7OCA: Glutamate receptor 1

Resting state full-length GluA1/A2 heterotertramer in complex with TARP gamma 8 and CNIH2. Determined by electron microscopy at 3.4 Å resolution. Released 9 Jun 2021.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 29,294
Mol. weight: 571.63 kDa
Ligands: E2Q, NAG, PC1, CLR
Released: 9 Jun 2021

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

Secondary structure: helices and β-sheets

7OCA contains 156 α-helices and 166 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: 32 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	9	1	2
β-strand	11-13	3	3
α-helix	19-29	11
β-strand	36-38	3	1
β-strand	41-43	3	3
α-helix	49-62	14
β-strand	66	1	2
β-strand	67-68	2	4
β-strand	69	1	3
α-helix	73-85	13
β-strand	90-92	3	4
β-strand	104-106	3	4
α-helix	112-121	10
β-strand	126-131	6	5
α-helix	137-150	14
β-strand	153-158	6	5
α-helix	164-175	12
β-strand	180-185	6	5
α-helix	188-200	13
β-strand	208-213	6	5
α-helix	223-225	3
β-strand	231-236	6	5
α-helix	243-258	16
α-helix	270-292	23
α-helix	311-313	3
α-helix	316-325	10
β-strand	328-329	2	6
β-strand	334-335	2	6
β-strand	342	1	4
β-strand	347-354	8	5
β-strand	357-365	9	5
β-strand	371-372	2	5
α-helix	388-390	3
β-strand	391-394	4	7
β-strand	398	1	8
β-strand	402	1	8
β-strand	403-404	2	9
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	9
α-helix	420-432	13
β-strand	436-438	3	7
β-strand	449	1	10
β-strand	456	1	10
α-helix	459-464	6
β-strand	470-476	7	7
α-helix	479-484	6
β-strand	485-486	2	11
β-strand	492-494	3	7
β-strand	496-501	6	12
α-helix	508-509	2
β-strand	517	1	13
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	12
β-strand	646	1	14
α-helix	650-656	7
α-helix	661-669	9
β-strand	679	1	14
α-helix	682-691	10
β-strand	696-701	6	12
α-helix	702-709	8
β-strand	716-719	4	12
β-strand	726-731	6	7
β-strand	732-733	2	11
α-helix	740-752	13
α-helix	754-763	10
β-strand	783	1	15
α-helix	784	1
α-helix	789-819	31

Chain B: 36 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	16
α-helix	17-30	14
β-strand	36-44	9	16
α-helix	49-61	13
β-strand	66-68	3	16
α-helix	76-86	11
β-strand	89-92	4	16
α-helix	95-97	3
β-strand	105-106	2	16
α-helix	109-110	2
α-helix	112-121	10
β-strand	126-131	6	17
α-helix	138-150	13
β-strand	153-158	6	17
α-helix	167-180	14
β-strand	185-189	5	17
α-helix	192-202	11
β-strand	213-216	4	17
β-strand	235-240	6	17
α-helix	247-257	11
α-helix	274-296	23
α-helix	314	1
α-helix	320-328	9
β-strand	332-333	2	18
β-strand	338-339	2	18
β-strand	340-341	2	19
β-strand	347-348	2	19
β-strand	353-358	6	17
β-strand	361-368	8	17
β-strand	374-376	3	17
β-strand	397-398	2	20
β-strand	407-408	2	21
α-helix	409	1
β-strand	421-422	2	21
α-helix	424-436	13
β-strand	452-453	2	22
β-strand	460-461	2	22
α-helix	462-468	7
β-strand	474-475	2	20
α-helix	479	1
β-strand	480	1	23
α-helix	481	1
α-helix	483-486	4
β-strand	489-491	3	20
β-strand	496-498	3	23
β-strand	500-505	6	24
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	15
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	24
β-strand	650	1	25
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	25
α-helix	686-695	10
β-strand	700-705	6	24
α-helix	706-712	7
β-strand	720-723	4	24
β-strand	730-732	3	23
β-strand	735-737	3	20
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	782-786	5
β-strand	787	1	26
α-helix	789-791	3
α-helix	793-821	29

Chain D: 36 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	28
α-helix	17-30	14
β-strand	36-44	9	28
α-helix	49-61	13
β-strand	66-68	3	28
α-helix	76-86	11
β-strand	89-92	4	28
α-helix	95-97	3
β-strand	105-106	2	28
α-helix	109-110	2
α-helix	112-121	10
β-strand	126-131	6	29
α-helix	138-150	13
β-strand	153-158	6	29
α-helix	167-180	14
β-strand	185-189	5	29
α-helix	192-202	11
β-strand	213-216	4	29
β-strand	235-240	6	29
α-helix	247-257	11
α-helix	274-296	23
α-helix	314	1
α-helix	320-328	9
β-strand	332-333	2	30
β-strand	338-339	2	30
β-strand	340-341	2	31
β-strand	347-348	2	31
β-strand	353-358	6	29
β-strand	361-368	8	29
β-strand	374-376	3	29
β-strand	398	1	32
β-strand	407-408	2	33
α-helix	409	1
β-strand	421-422	2	33
α-helix	424-436	13
β-strand	452-453	2	34
β-strand	460-461	2	34
α-helix	462-468	7
β-strand	475	1	32
α-helix	479	1
β-strand	480	1	35
α-helix	481	1
α-helix	483-486	4
β-strand	489-491	3	32
β-strand	496-498	3	35
β-strand	500-505	6	36
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	37
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	36
β-strand	650	1	38
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	38
α-helix	686-695	10
β-strand	700-705	6	36
α-helix	706-712	7
β-strand	720-723	4	36
β-strand	730-732	3	35
β-strand	735-737	3	32
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	782-786	5
β-strand	787	1	13
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	27
β-strand	80-84	5	27
β-strand	88-91	4	27
β-strand	100-102	3	27
α-helix	116-127	12
α-helix	129-148	20
α-helix	158-183	26
β-strand	200-201	2	27
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	423	Rattus norvegicus	Q8VHW5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7OCA_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

>7OCA_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

>7OCA_3 Protein cornichon homolog 2 (chains E, G)
MAFTFAAFCYMLTLVLCASLIFFVIWHIIAFDELRTDFKNPIDQGNPARARERLKNIERI
CCLLRKLVVPEYSIHGLFCLMFLCAAEWVTLGLNIPLLFYHLWRYFHRPADGSEVMYDAV
SIMNADILNYCQKESWCKLAFYLLSFFYYLYSMVYTLVSFENLYFQSGGSTETSQVAPAY
PYDVPDYA

Sequence of entity 4 (I, J), FASTA

>7OCA_4 Voltage-dependent calcium channel gamma-8 subunit (chains I, J)
GESLKRWNEERGLWCEKGVQVLLTTIGAFAAFGLMTIAISTDYWLYTRALICNTTNLTAG
DDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYL
LRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYI
SANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSD
LLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFA
STDISMYTLSRDPSKGSVAAGLASAGGGGGGAGVGAYGGAAGAAGGGGTGSERDRGSSAG
FLTLHNAFPKEAASGVTVTVTGPPAAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKLEV
LFQ

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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
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
7OCE 3.1 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD)
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

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