6QKZ: Full length GluA1/2-gamma8 complex

Full length GluA1/2-gamma8 complex. Determined by electron microscopy at 6.3 Å resolution. Released 27 Mar 2019.

Method: Electron microscopy
Resolution: 6.3 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 13,949
Mol. weight: 481.93 kDa
Ligands: NAG, E2Q
Released: 27 Mar 2019

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

Secondary structure: helices and β-sheets

6QKZ contains 150 α-helices and 166 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: 35 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	19-30	12
β-strand	36-43	8	1
α-helix	49-62	14
β-strand	67-69	3	1
α-helix	76-86	11
β-strand	90-92	3	1
α-helix	95-97	3
β-strand	104-106	3	1
α-helix	109-110	2
α-helix	112-121	10
β-strand	126-131	6	2
α-helix	138-150	13
β-strand	153-158	6	2
α-helix	159-161	3
α-helix	164-174	11
β-strand	180-185	6	2
α-helix	188-202	15
β-strand	208-213	6	2
β-strand	216	1	2
α-helix	217-219	3
α-helix	222-225	4
β-strand	231-236	6	2
α-helix	243-258	16
α-helix	267-269	3
α-helix	270-291	22
α-helix	316-324	9
β-strand	327-330	4	3
β-strand	333-336	4	3
β-strand	337	1	4
β-strand	342	1	1
β-strand	343	1	4
β-strand	347-353	7	2
β-strand	359-365	7	2
β-strand	369-372	4	2
β-strand	392-395	4	5
β-strand	403-404	2	6
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	6
α-helix	420-432	13
β-strand	437-440	4	5
β-strand	447-449	3	7
β-strand	456-458	3	7
α-helix	459-465	7
β-strand	470-471	2	5
β-strand	476	1	8
α-helix	479-484	6
β-strand	486-487	2	5
β-strand	493-494	2	9
β-strand	496-501	6	10
α-helix	507-509	3
β-strand	517	1	11
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	10
β-strand	646	1	12
α-helix	650-656	7
α-helix	663-671	9
β-strand	679	1	12
α-helix	682-692	11
β-strand	696-701	6	10
α-helix	702-710	9
β-strand	716-719	4	10
β-strand	726-727	2	9
β-strand	728	1	8
β-strand	731-732	2	5
α-helix	739-752	14
α-helix	755-760	6
α-helix	761-765	5
β-strand	783	1	13
α-helix	789-812	24

Chains B and D: 34 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	14
α-helix	17-30	14
β-strand	36-44	9	14
α-helix	49-62	14
β-strand	67-69	3	14
α-helix	76-86	11
β-strand	90-92	3	14
α-helix	95-97	3
β-strand	104-106	3	14
α-helix	109-110	2
α-helix	112-121	10
β-strand	126-131	6	15
α-helix	138-146	9
β-strand	153-158	6	15
α-helix	168-175	8
β-strand	185-187	3	15
α-helix	192-205	14
β-strand	209	1	16
β-strand	213-216	4	15
β-strand	220	1	15
α-helix	221-223	3
α-helix	227-229	3
β-strand	233	1	16
β-strand	235-240	6	15
α-helix	247-256	10
α-helix	274-295	22
α-helix	320-329	10
β-strand	332-334	3	17
β-strand	337-339	3	17
β-strand	341	1	18
β-strand	346	1	14
β-strand	347	1	18
β-strand	351-358	8	15
β-strand	361-369	9	15
β-strand	373-376	4	15
β-strand	397-399	3	19
β-strand	407-408	2	20
α-helix	409	1
β-strand	421-422	2	20
α-helix	424-432	9
β-strand	442-444	3	19
α-helix	462-468	7
β-strand	474-480	7	19
α-helix	483-488	6
β-strand	490-491	2	19
β-strand	496-498	3	19
β-strand	500-505	6	21
α-helix	510-512	3
β-strand	521	1	13
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	21
β-strand	649-650	2	22
α-helix	654-660	7
α-helix	665-675	11
β-strand	682-683	2	22
α-helix	686-696	11
β-strand	700-705	6	21
α-helix	706-714	9
β-strand	720-723	4	21
β-strand	730-736	7	19
α-helix	743-756	14
α-helix	759-764	6
α-helix	765-769	5
α-helix	784-786	3
β-strand	787	1	23
α-helix	788	1
α-helix	789-791	3
α-helix	793-818	26

Chain C: 35 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	24
α-helix	19-30	12
β-strand	36-43	8	24
α-helix	49-62	14
β-strand	67-69	3	24
α-helix	76-86	11
β-strand	90-92	3	24
α-helix	95-97	3
β-strand	104-106	3	24
α-helix	109-110	2
α-helix	112-121	10
β-strand	126-131	6	25
α-helix	138-150	13
β-strand	153-158	6	25
α-helix	159-161	3
α-helix	164-174	11
β-strand	180-185	6	25
α-helix	188-202	15
β-strand	208-213	6	25
β-strand	216	1	25
α-helix	217-219	3
α-helix	222-225	4
β-strand	231-236	6	25
α-helix	243-258	16
α-helix	267-269	3
α-helix	270-291	22
α-helix	316-324	9
β-strand	327-330	4	26
β-strand	333-336	4	26
β-strand	337	1	27
β-strand	342	1	24
β-strand	343	1	27
β-strand	347-353	7	25
β-strand	359-365	7	25
β-strand	369-372	4	25
β-strand	392-395	4	28
β-strand	398	1	29
β-strand	402	1	29
β-strand	403	1	30
α-helix	404-405	2
α-helix	408-410	3
α-helix	413-416	4
β-strand	418	1	30
α-helix	420-432	13
β-strand	437-440	4	28
β-strand	447-449	3	31
β-strand	456-458	3	31
α-helix	459-465	7
β-strand	470-471	2	28
β-strand	476	1	32
α-helix	479-484	6
β-strand	486-487	2	28
β-strand	493-494	2	33
β-strand	496-501	6	34
α-helix	507-509	3
β-strand	517	1	23
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	34
β-strand	646	1	35
α-helix	650-656	7
α-helix	663-671	9
β-strand	679	1	35
α-helix	682-692	11
β-strand	696-701	6	34
α-helix	702-710	9
β-strand	716-719	4	34
β-strand	726-727	2	33
β-strand	728	1	32
β-strand	731-732	2	28
α-helix	739-752	14
α-helix	755-760	6
α-helix	761-765	5
β-strand	783	1	36
α-helix	789-812	24

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

Element	Residues	Length	Sheet
α-helix	19-39	21
β-strand	44-45	2	46
β-strand	80-83	4	46
β-strand	87-91	5	46
β-strand	100-101	2	46
α-helix	117-125	9
α-helix	128-148	21
α-helix	157-182	26
α-helix	196-198	3
β-strand	199-200	2	46
α-helix	202-229	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GluA1	A, C	protein	897	Rattus norvegicus	P19490 (AlphaFold model)
Glutamate receptor 2	B, D	protein	839	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

>6QKZ_1 GluA1 (chains A, C)
ADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEM
TYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPELQ
EALISIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQVTAVNILTTTEEGYRMLFQ
DLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILANLGFMDIDLNKFKESGANV
TGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQ
RIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIE
MKHDGIRKIGYWNEDDKFVPAATDAQAGGDNSSVQNRTYIVTTILEDPYVMLKKNANQFE
GNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTKAWNGMVGELVYGRADVAV
APLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGV
SVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLWFSLGAFMQQGCDISPRSL
SGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLEAGSTK
EFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKGKYAYLLESTMNEYIEQRK
PCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGVLDKLKSKWWYDKGECGSK
DSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKSRSESKRMKGFCLIPQQSI
NEAIRTSTLPRNSGAGASGGGGSGENGRVVSQDFPKSMQSIPCMSHSSGMPLGATGL

Sequence of entity 2 (B, D), FASTA

>6QKZ_2 Glutamate receptor 2 (chains B, D)
VSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQF
SRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIE
YYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLEL
KKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGANVSGFQ
IVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEI
SRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTN
GPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTTILESPYVMMKKNHEMLEGNER
YEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLT
ITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVL
FLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMRQGCDISPRSLSGRI
VGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFR
RSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDT
MKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGAKDSGS
KEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKVAKNPQNINPSSS

Sequence of entity 3 (I, J), FASTA

>6QKZ_3 Voltage-dependent calcium channel gamma-8 subunit (chains I, J)
GESLKRWNEERGLWCEKGVQVLLTTIGAFAAFGLMTIAISTDYWLYTRALICNTTNLTAG
DDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSSEYL
LRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYI
SANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSD
LLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFA
STDISMYTLSRDPSKGSVAAGLASAGGGGGGAGVGAYGGAAGAAGGGGTGSERDRGSSAG
FLTLHNAFPKEAASGVTVTVTGPPAAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKLEV
LFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
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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