7OCD: Resting state GluA1/A2 heterotetramer

Resting state GluA1/A2 heterotetramer in complex with auxiliary subunit TARP gamma 8 (LBD-TMD). Determined by electron microscopy at 3.5 Å resolution. Released 9 Jun 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 13,624
Mol. weight: 491.06 kDa
Ligands: E2Q, PC1
Released: 9 Jun 2021

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

Secondary structure: helices and β-sheets

7OCD contains 96 α-helices and 88 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: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	392-395	4	1
β-strand	403-404	2	2
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	2
α-helix	420-432	13
β-strand	437-440	4	1
β-strand	449	1	3
β-strand	456	1	3
α-helix	459-464	6
β-strand	470-471	2	1
β-strand	476	1	4
α-helix	479-484	6
β-strand	485	1	5
β-strand	492-494	3	4
β-strand	496-501	6	6
α-helix	507-509	3
α-helix	512-514	3
β-strand	517	1	7
α-helix	519-541	23
α-helix	569-580	12
α-helix	592-622	31
α-helix	632-636	5
β-strand	642-644	3	6
β-strand	646	1	8
α-helix	650-656	7
α-helix	661-671	11
α-helix	674	1
α-helix	676	1
β-strand	679	1	8
α-helix	682-691	10
β-strand	696-701	6	6
α-helix	702-708	7
β-strand	716-719	4	6
β-strand	726-728	3	4
β-strand	731	1	1
β-strand	733	1	5
α-helix	739-751	13
α-helix	755-760	6
α-helix	761-765	5
β-strand	783	1	9
α-helix	784	1
α-helix	785-787	3
α-helix	789-813	25

Chains B and D: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	398-399	2	27
β-strand	407-408	2	28
α-helix	409	1
β-strand	421-422	2	28
α-helix	424-436	13
β-strand	443-444	2	27
α-helix	462-468	7
β-strand	475	1	27
β-strand	480	1	29
α-helix	483-486	4
β-strand	489	1	30
β-strand	496-498	3	29
β-strand	500-505	6	31
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	636-640	5
β-strand	646-648	3	31
β-strand	650	1	32
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	32
α-helix	686-695	10
β-strand	700-705	6	31
α-helix	706-712	7
β-strand	720-723	4	31
β-strand	730-732	3	29
β-strand	735	1	27
β-strand	737	1	30
α-helix	743-756	14
α-helix	759-763	5
α-helix	764-769	6
β-strand	787	1	16
α-helix	789-818	30

Chain C: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	392-395	4	10
β-strand	403-404	2	11
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	11
α-helix	420-432	13
β-strand	437-440	4	10
β-strand	448-449	2	12
β-strand	456-457	2	12
α-helix	459-464	6
β-strand	470-471	2	10
β-strand	476	1	13
α-helix	479-484	6
β-strand	485	1	14
β-strand	492-494	3	13
β-strand	496-501	6	15
α-helix	507-509	3
α-helix	512-514	3
β-strand	517	1	16
α-helix	519-541	23
α-helix	569-580	12
α-helix	592-622	31
α-helix	632-636	5
β-strand	642-644	3	15
β-strand	646	1	17
α-helix	650-656	7
α-helix	661-671	11
α-helix	674	1
α-helix	676	1
β-strand	679	1	17
α-helix	682-691	10
β-strand	696-701	6	15
α-helix	702-708	7
β-strand	716-719	4	15
β-strand	726-728	3	13
β-strand	731	1	10
β-strand	733	1	14
α-helix	739-751	13
α-helix	755-760	6
α-helix	761-765	5
β-strand	783	1	18
α-helix	784	1
α-helix	785-787	3
α-helix	789-813	25

Chains I and J: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-40	21
β-strand	45-48	4	25
β-strand	81-84	4	25
β-strand	90-91	2	25
α-helix	118-126	9
α-helix	129-149	21
α-helix	157-183	27
β-strand	199-201	3	25
α-helix	203-230	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 1	A, C	protein	915	Rattus norvegicus	P19490 (AlphaFold model)
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)

Sequence of entity 1 (A, C), FASTA

>7OCD_1 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

Sequence of entity 2 (B, D), FASTA

>7OCD_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 (I, J), FASTA

>7OCD_3 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
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	6

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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