8P3W: Glutamate receptor 1 flip isoform

Homomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 4. Determined by electron microscopy at 3.53 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.53 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 17,485
Mol. weight: 559.4 kDa
Ligands: POV, OLC, PLM
Released: 30 Aug 2023

Explore 8P3W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P3W contains 117 α-helices and 112 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.

Chain A: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	390-395	6	1
β-strand	398	1	2
β-strand	402	1	2
β-strand	403-404	2	3
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	3
α-helix	420-432	13
β-strand	435-440	6	1
α-helix	441	1
β-strand	447-449	3	4
β-strand	456-457	2	4
α-helix	458-465	8
β-strand	470-471	2	1
α-helix	475	1
β-strand	476	1	5
α-helix	477	1
α-helix	479-482	4
β-strand	485-487	3	1
β-strand	492-494	3	5
β-strand	496-501	6	6
α-helix	512-514	3
β-strand	517	1	7
α-helix	519-541	23
α-helix	569-580	12
α-helix	592-625	34
α-helix	632-637	6
β-strand	642-644	3	6
β-strand	646	1	8
α-helix	650-656	7
α-helix	661-672	12
β-strand	679	1	8
α-helix	682-690	9
β-strand	696-701	6	6
α-helix	702-709	8
β-strand	716-719	4	6
β-strand	724	1	9
β-strand	726-728	3	5
β-strand	731-733	3	1
α-helix	739-751	13
α-helix	754-759	6
α-helix	760-764	5
α-helix	782	1
β-strand	783	1	10
α-helix	784	1
α-helix	785-788	4
α-helix	789-813	25

Chain B: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	391-395	5	11
β-strand	403-404	2	12
α-helix	405	1
α-helix	408-410	3
α-helix	414-416	3
β-strand	417-418	2	12
α-helix	420-432	13
β-strand	436-440	5	11
α-helix	441	1
β-strand	449	1	13
β-strand	456	1	13
α-helix	458-464	7
β-strand	470-471	2	11
α-helix	475	1
β-strand	476	1	14
α-helix	477	1
α-helix	479-482	4
β-strand	485-487	3	11
β-strand	492-494	3	14
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	632-637	6
β-strand	642-644	3	15
β-strand	646	1	17
α-helix	650-656	7
α-helix	661-672	12
β-strand	679	1	17
α-helix	682-691	10
β-strand	696-701	6	15
α-helix	702-710	9
β-strand	716-719	4	15
β-strand	726-728	3	14
β-strand	731-733	3	11
α-helix	739-751	13
α-helix	754-759	6
α-helix	760-764	5
α-helix	782	1
β-strand	783	1	7
α-helix	784	1
α-helix	785-788	4
α-helix	789-814	26

Chain C: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	390-395	6	18
β-strand	398	1	19
β-strand	402	1	19
β-strand	403-404	2	20
α-helix	405	1
α-helix	408-410	3
α-helix	413-416	4
β-strand	417-418	2	20
α-helix	420-432	13
β-strand	435-440	6	18
α-helix	441	1
β-strand	447-449	3	21
β-strand	456-457	2	21
α-helix	458-465	8
β-strand	470-471	2	18
α-helix	475	1
β-strand	476	1	22
α-helix	477	1
α-helix	479-482	4
β-strand	485-487	3	18
β-strand	492-494	3	22
β-strand	496-500	5	23
α-helix	508-509	2
α-helix	512-514	3
β-strand	517	1	24
α-helix	519-541	23
α-helix	569-580	12
α-helix	592-621	30
α-helix	632-637	6
β-strand	642-644	3	23
β-strand	646	1	25
α-helix	650-656	7
α-helix	661-671	11
β-strand	679	1	25
α-helix	682-690	9
β-strand	696-701	6	23
α-helix	702-710	9
β-strand	717-719	3	23
β-strand	726-728	3	22
β-strand	731-733	3	18
α-helix	739-751	13
α-helix	754-763	10
β-strand	783	1	16
α-helix	785-787	3
α-helix	789-813	25

Chain D: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	391-395	5	26
β-strand	398	1	27
β-strand	402	1	27
β-strand	403-404	2	28
α-helix	405	1
α-helix	413-416	4
β-strand	417-418	2	28
α-helix	420-432	13
β-strand	436-440	5	26
α-helix	441	1
β-strand	449	1	29
β-strand	456	1	29
α-helix	458-465	8
β-strand	470-471	2	26
α-helix	475	1
β-strand	476	1	30
α-helix	477	1
α-helix	479-482	4
β-strand	485-487	3	26
β-strand	492-494	3	30
β-strand	496-501	6	31
α-helix	512-514	3
β-strand	517	1	10
α-helix	519-541	23
α-helix	569-580	12
α-helix	592-621	30
α-helix	632-637	6
β-strand	642-644	3	31
β-strand	646	1	32
α-helix	650-656	7
β-strand	660	1	9
α-helix	661-672	12
β-strand	679	1	32
α-helix	682-691	10
β-strand	696-701	6	31
α-helix	702-710	9
β-strand	716-719	4	31
β-strand	726-728	3	30
β-strand	731-733	3	26
α-helix	739-751	13
α-helix	754-763	10
α-helix	782	1
β-strand	783	1	24
α-helix	784	1
α-helix	785-788	4
α-helix	789-814	26

Chains E and G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-35	2	33
β-strand	37-38	2	34
β-strand	57-58	2	34
β-strand	59-61	3	33
β-strand	65-68	4	33
β-strand	77-79	3	33
α-helix	93-104	12
α-helix	106-127	22
α-helix	133-161	29
β-strand	174-175	2	33
α-helix	177-208	32

Chains F and H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-38	5	35
β-strand	57-61	5	35
β-strand	65-68	4	35
β-strand	77-79	3	35
α-helix	93-104	12
α-helix	106-125	20
α-helix	133-161	29
β-strand	173-175	3	35
α-helix	177-208	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 1 flip isoform	A, B, C, D	protein	915	Rattus norvegicus	P19490 (AlphaFold model)
Voltage-dependent calcium channel gamma-3 subunit	E, F, G, H	protein	314	Rattus norvegicus	Q8VHX0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8P3W_1 Glutamate receptor 1 flip isoform (chains A, B, C, D)
MPYIFAFFCTGFLGAVVGADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEP
PKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPS
FPVDTSNQFVLQLRPELQEALISIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQV
TAVNILTTTEEGYRMLFQDLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILAN
LGFMDIDLNKFKESGANVTGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSAL
TYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGN
VQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAATDAQAGGDNSSVQNRTYIVT
TILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTK
AWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL
DPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLW
FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED
LAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKG
KYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGV
LDKLKSKWWYDKGECGSKDSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKS
RSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGGGSGENGRVVSQDFPKSMQSIP
CMSHSSGMPLGATGL

Sequence of entity 2 (E, F, G, H), FASTA

>8P3W_2 Voltage-dependent calcium channel gamma-3 subunit (chains E, F, G, H)
RMCDRGIQMLITTVGAFAAFSLMTIAVGTDYWLYSRGVCRTKSTSDNETSRKNEEVMTHS
GLWRTCCLEGAFRGVCKKIDHFPEDADYEQDTAEYLLRAVRASSVFPILSVTLLFFGGLC
VAASEFHRSRHSVILSAGIFFVSAGLSNIIGIIVYISANAGDPGQRDSKKSYSYGWSFYF
GAFSFIIAEIVGVVAVHIYIEKHQQLRARSHSELLKKSTFARLPPYRYRFRRRSSSRSTE
PRSRDLSPISKGFHTIPSTDISMFTLSRDPSKLTMGTLLNSDRDHAFLQFHNSTPKEFKE
SLHNNPANRRTTPV

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	6
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4
PLM	Palmitic acid	C16 H32 O2	4

Primary citation

Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. Zhang, D., Ivica, J., Krieger, J.M. et al. Nature (2023) 621:877-882. DOI 10.1038/s41586-023-06528-0 · 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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