6QKC: GluA1/2

GluA1/2 In complex with auxiliary subunit gamma-8. Determined by electron microscopy at 4.4 Å resolution. Released 27 Mar 2019.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 13,794
Mol. weight: 490.59 kDa
Ligands: OLC, E2Q
Released: 27 Mar 2019

Explore 6QKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QKC contains 88 α-helices and 86 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.

Chains A and C: 18 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	447-449	3	3
β-strand	456-458	3	3
α-helix	459-465	7
β-strand	470-471	2	1
β-strand	476	1	4
α-helix	479-484	6
β-strand	486-487	2	1
β-strand	493-494	2	5
β-strand	496-501	6	6
β-strand	517	1	7
α-helix	519-540	22
α-helix	571-580	10
α-helix	592-624	33
α-helix	632-636	5
β-strand	642-644	3	6
β-strand	646	1	8
α-helix	650-656	7
α-helix	663-671	9
β-strand	679	1	8
α-helix	682-692	11
β-strand	696-701	6	6
α-helix	702-710	9
β-strand	716-719	4	6
β-strand	726-727	2	5
β-strand	728	1	4
β-strand	731-732	2	1
α-helix	739-752	14
α-helix	755-760	6
α-helix	761-765	5
β-strand	783	1	9
α-helix	790-812	23

Chain B: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	397-399	3	10
β-strand	407-408	2	11
α-helix	409	1
β-strand	421-422	2	11
α-helix	424-432	9
β-strand	442-444	3	10
α-helix	462-468	7
β-strand	474-475	2	10
β-strand	480	1	12
α-helix	483-488	6
β-strand	490-491	2	10
β-strand	496-498	3	12
β-strand	500-505	6	13
α-helix	516-518	3
β-strand	521	1	9
α-helix	523-544	22
α-helix	573-584	12
α-helix	596-623	28
α-helix	638-642	5
β-strand	646-648	3	13
β-strand	649-650	2	14
α-helix	654-660	7
α-helix	665-675	11
β-strand	682-683	2	14
α-helix	686-696	11
β-strand	700-705	6	13
α-helix	706-714	9
β-strand	720-723	4	13
β-strand	730-732	3	12
β-strand	735-736	2	10
α-helix	743-756	14
α-helix	759-764	6
α-helix	765-769	5
α-helix	784-786	3
β-strand	787	1	15
α-helix	788	1
α-helix	789-791	3
α-helix	793-818	26

Chain D: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	397-399	3	24
β-strand	407-408	2	25
α-helix	409	1
β-strand	421-422	2	25
α-helix	424-432	9
β-strand	442-444	3	24
α-helix	462-468	7
β-strand	474-480	7	24
α-helix	483-488	6
β-strand	490-491	2	24
β-strand	496-498	3	24
β-strand	500-505	6	26
α-helix	516-518	3
β-strand	521	1	23
α-helix	523-544	22
α-helix	573-584	12
α-helix	596-623	28
α-helix	638-642	5
β-strand	646-648	3	26
β-strand	649-650	2	27
α-helix	654-660	7
α-helix	665-675	11
β-strand	682-683	2	27
α-helix	686-696	11
β-strand	700-705	6	26
α-helix	706-714	9
β-strand	720-723	4	26
β-strand	730-736	7	24
α-helix	743-756	14
α-helix	759-764	6
α-helix	765-769	5
α-helix	784-786	3
β-strand	787	1	7
α-helix	788	1
α-helix	789-791	3
α-helix	793-818	26

Chains I and J: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	20-40	21
β-strand	45-46	2	28
β-strand	81-84	4	28
β-strand	88-92	5	28
β-strand	101-102	2	28
α-helix	118-126	9
α-helix	129-149	21
α-helix	158-183	26
α-helix	197-199	3
β-strand	200-201	2	28
α-helix	203-230	28

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)
Voltage-dependent calcium channel gamma-8 subunit	I, J	protein	423	Rattus norvegicus	Q8VHW5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6QKC_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

>6QKC_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

>6QKC_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
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	12
E2Q	6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide	C12 H8 N4 O6 S	4

Primary citation

Architecture of the heteromeric GluA1/2 AMPA receptor in complex with the auxiliary subunit TARP gamma 8. Herguedas, B., Watson, J.F., Ho, H. et al. Science (2019) 364. DOI 10.1126/science.aav9011 · 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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