7OCF: Active state GluA1/A2 AMPA receptor

Active state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD). Determined by electron microscopy at 3.6 Å resolution. Released 9 Jun 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 17,088
Mol. weight: 551.66 kDa
Ligands: GLU, PC1, CYZ
Released: 9 Jun 2021

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

Secondary structure: helices and β-sheets

7OCF contains 100 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	392	1	1
β-strand	393	1	2
β-strand	395	1	3
β-strand	404	1	4
α-helix	414-416	3
β-strand	417	1	4
α-helix	420-432	13
β-strand	437	1	1
β-strand	440	1	3
α-helix	459-464	6
β-strand	470	1	2
β-strand	471	1	5
α-helix	479-482	4
β-strand	486-487	2	5
β-strand	493-494	2	6
β-strand	496-501	6	7
α-helix	502-505	4
α-helix	512-514	3
β-strand	517	1	8
α-helix	519-540	22
α-helix	544-547	4
α-helix	570-580	11
α-helix	592-620	29
α-helix	622-624	3
α-helix	632-637	6
β-strand	642-645	4	7
α-helix	650-657	8
α-helix	661-671	11
α-helix	682-691	10
β-strand	696-701	6	7
α-helix	704-709	6
β-strand	716-719	4	7
β-strand	726-727	2	6
β-strand	731-732	2	5
α-helix	740-751	12
α-helix	754-759	6
α-helix	760-764	5
β-strand	783	1	9
α-helix	785-814	30

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

Element	Residues	Length	Sheet
β-strand	397-399	3	10
β-strand	407-408	2	11
α-helix	412-414	3
α-helix	417-419	3
β-strand	421-422	2	11
α-helix	424-436	13
β-strand	442-444	3	10
β-strand	453	1	12
β-strand	460	1	12
α-helix	463-468	6
β-strand	475	1	13
β-strand	480	1	14
α-helix	483-486	4
β-strand	489-491	3	13
β-strand	501-503	3	15
β-strand	504-505	2	16
α-helix	510-512	3
β-strand	521	1	9
α-helix	523-545	23
α-helix	574-584	11
α-helix	596-617	22
α-helix	621-625	5
α-helix	636-641	6
β-strand	646-649	4	15
β-strand	650	1	17
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	17
α-helix	686-693	8
β-strand	700-704	5	15
α-helix	706-714	9
β-strand	720-721	2	16
β-strand	732	1	14
β-strand	735-737	3	13
α-helix	743-755	13
α-helix	758-766	9
α-helix	786	1
β-strand	787	1	18
α-helix	788	1
α-helix	793-818	26

Chains E and G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-39	35
α-helix	50-84	35
α-helix	89-106	18
α-helix	125-158	34

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

Element	Residues	Length	Sheet
α-helix	20-41	22
β-strand	45-49	5	19
β-strand	80-82	3	19
β-strand	88-90	3	20
β-strand	91	1	19
β-strand	100-102	3	20
α-helix	112-114	3
α-helix	116-127	12
α-helix	129-148	20
α-helix	156-185	30
β-strand	199-201	3	19
α-helix	203-232	30

Molecules and chains

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

>7OCF_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

>7OCF_2 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 3 (E, G), FASTA

>7OCF_3 Protein cornichon homolog 2 (chains E, G)
MAFTFAAFCYMLTLVLCASLIFFVIWHIIAFDELRTDFKNPIDQGNPARARERLKNIERI
CCLLRKLVVPEYSIHGLFCLMFLCAAEWVTLGLNIPLLFYHLWRYFHRPADGSEVMYDAV
SIMNADILNYCQKESWCKLAFYLLSFFYYLYSMVYTLVSFENLYFQSGGSTETSQVAPAY
PYDVPDYA

Sequence of entity 4 (I, J), FASTA

>7OCF_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
GLU	Glutamic acid	C5 H9 N O4	4
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	26
CYZ	Cyclothiazide	C14 H16 Cl N3 O4 S2	4

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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