9B5Z: GluA2 flip Q

GluA2 flip Q in complex with TARPgamma2 at pH8, consensus structure of LBD-TMD-TARPgamma2. Determined by electron microscopy at 2.71 Å resolution. Released 31 Jul 2024.

Method: Electron microscopy
Resolution: 2.71 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 8
Atoms: 18,680
Mol. weight: 542.22 kDa
Released: 31 Jul 2024

Explore 9B5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B5Z contains 113 α-helices and 103 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: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	395-399	5	19
β-strand	402	1	20
β-strand	406	1	20
β-strand	407	1	21
α-helix	417-420	4
β-strand	422	1	21
α-helix	424-436	13
β-strand	440-444	5	19
β-strand	453-454	2	22
β-strand	459-460	2	22
α-helix	462-468	7
β-strand	474	1	19
β-strand	475	1	23
β-strand	480	1	24
α-helix	483-486	4
β-strand	489-491	3	23
β-strand	496-498	3	24
β-strand	500-505	6	25
α-helix	506-508	3
α-helix	511-513	3
α-helix	516-518	3
β-strand	521	1	18
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-629	34
α-helix	636-641	6
β-strand	646-648	3	25
β-strand	650	1	26
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	26
α-helix	686-695	10
β-strand	700-705	6	25
α-helix	706-713	8
β-strand	720-723	4	25
β-strand	730-732	3	24
β-strand	735-737	3	23
α-helix	743-756	14
α-helix	758-764	7
α-helix	765-769	5
β-strand	787	1	27
α-helix	788	1
α-helix	789-791	3
α-helix	793-824	32

Chain B: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	394-399	6	11
β-strand	402	1	12
β-strand	406	1	12
β-strand	407-408	2	13
α-helix	417-420	4
β-strand	421-422	2	13
α-helix	424-436	13
β-strand	439-444	6	11
β-strand	453	1	14
β-strand	460	1	14
α-helix	462-468	7
β-strand	474-475	2	11
α-helix	479	1
β-strand	480	1	15
α-helix	481	1
α-helix	483-486	4
β-strand	490-491	2	11
β-strand	496-498	3	15
β-strand	500-505	6	16
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	10
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-625	30
α-helix	636-641	6
β-strand	646-648	3	16
β-strand	650	1	17
α-helix	654-660	7
α-helix	665-675	11
β-strand	683	1	17
α-helix	686-694	9
β-strand	700-705	6	16
α-helix	706-713	8
β-strand	720-723	4	16
β-strand	730-732	3	15
β-strand	735-736	2	11
α-helix	743-756	14
α-helix	758-764	7
α-helix	765-769	5
α-helix	785-786	2
β-strand	787	1	18
α-helix	788	1
α-helix	789-791	3
α-helix	793-824	32

Chain C: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	394	1
β-strand	395-399	5	3
β-strand	402	1	4
β-strand	406	1	4
β-strand	407-408	2	5
α-helix	418-420	3
β-strand	421-422	2	5
α-helix	424-436	13
β-strand	440-444	5	3
β-strand	454	1	6
β-strand	459	1	6
α-helix	462-468	7
β-strand	474-480	7	3
α-helix	483-486	4
β-strand	489-491	3	3
β-strand	496-498	3	3
β-strand	500-505	6	7
α-helix	516-518	3
β-strand	521	1	8
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-629	34
α-helix	636-641	6
β-strand	646-648	3	7
β-strand	650	1	9
α-helix	654-661	8
α-helix	665-675	11
β-strand	683	1	9
α-helix	686-695	10
β-strand	700-705	6	7
α-helix	706-713	8
β-strand	720-723	4	7
β-strand	730-737	8	3
α-helix	743-756	14
α-helix	758-764	7
α-helix	765-769	5
β-strand	787	1	10
α-helix	788	1
α-helix	789-792	4
α-helix	793-824	32

Chain D: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	396-399	4	28
β-strand	407-408	2	29
α-helix	417-420	4
β-strand	421-422	2	29
α-helix	424-436	13
β-strand	441-444	4	28
β-strand	453	1	30
β-strand	460	1	30
α-helix	462-468	7
β-strand	474-480	7	28
α-helix	483-486	4
β-strand	489-491	3	28
β-strand	496-498	3	28
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	27
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-625	30
α-helix	636-641	6
β-strand	646-648	3	31
β-strand	650	1	32
α-helix	654-661	8
α-helix	665-675	11
β-strand	683	1	32
α-helix	686-694	9
β-strand	700-705	6	31
α-helix	706-713	8
β-strand	720-723	4	31
β-strand	730-737	8	28
α-helix	743-756	14
α-helix	758-764	7
α-helix	765-769	5
α-helix	785-786	2
β-strand	787	1	8
α-helix	788	1
α-helix	789-791	3
α-helix	793-824	32

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-38	5	33
β-strand	57-61	5	33
β-strand	65-68	4	33
β-strand	77-79	3	33
α-helix	93-104	12
α-helix	106-126	21
α-helix	133-160	28
β-strand	175-176	2	33
α-helix	178-213	36

Chain F: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-39	6	2
β-strand	56-61	6	2
β-strand	65-68	4	2
β-strand	77-79	3	2
α-helix	80-81	2
α-helix	93-104	12
α-helix	106-127	22
α-helix	133-160	28
α-helix	164-166	3
β-strand	175-176	2	2
α-helix	178-213	36

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-38	5	34
β-strand	57-61	5	34
β-strand	65-68	4	34
β-strand	77-79	3	34
α-helix	93-104	12
α-helix	106-124	19
α-helix	133-160	28
β-strand	174-176	3	34
α-helix	178-213	36

Chain H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-38	5	1
β-strand	57-61	5	1
β-strand	65-68	4	1
β-strand	77-79	3	1
α-helix	93-104	12
α-helix	106-127	22
α-helix	133-162	30
β-strand	175-176	2	1
α-helix	178-213	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-dependent calcium channel gamma-2 subunit	E, F, G, H	protein	323	Mus musculus	O88602 (AlphaFold model)
Isoform Flip of Glutamate receptor 2	A, B, C, D	protein	889	Rattus norvegicus	P19491 (AlphaFold model)

Sequence of entity 1 (E, F, G, H), FASTA

>9B5Z_1 Voltage-dependent calcium channel gamma-2 subunit (chains E, F, G, H)
MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTH
SGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGL
CIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSF
YFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSS
SRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVH
NCIQKDSKDSLHANTANRRTTPV

Sequence of entity 2 (A, B, C, D), FASTA

>9B5Z_2 Isoform Flip of Glutamate receptor 2 (chains A, B, C, D)
MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTP
HIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDG
THPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINV
GNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANL
GFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALT
YDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNI
KFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTT
ILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLD
PLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWF
SLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDL
SKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGK
YAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYDIATPKGSSLGTPVNLAVLKLSEQGVL
DKLKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSR
AEAKRMKVAKNPQNINPSSSQNSQNFATDYKDDDDKEGYNVYGIESVKI

Primary citation

Proton-triggered rearrangement of the AMPA receptor N-terminal domains impacts receptor kinetics and synaptic localization. Ivica, J., Kejzar, N., Ho, H. et al. Nat Struct Mol Biol (2024) 31:1601-1613. DOI 10.1038/s41594-024-01369-5 · PubMed

Other PDB entries of the same protein (UniProt O88602 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3JXT 1.5 Å, Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic…
8FQF 2.29 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2,…
8VHV 2.3 Å, Transmembrane AMPA Receptor Regulatory Protein Subunit Gamma 2
8FPG 2.32 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2,…
8FQ5 2.34 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with…
8FQB 2.36 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with…
8FPS 2.38 Å, GluA2 flip Q isoform N619K mutant of AMPA receptor in complex with gain-of-function TARP…
8FP4 2.4 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2,…
4X3H 2.4 Å, Crystal structure of arc N-lobe complexed with stargazin peptide
8FP9 2.44 Å, GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2,…
9B60 2.57 Å, GluA2 flip Q in complex with TARPgamma2 at pH8, consensus structure of TMD-TARPgamma2
9B63 2.76 Å, GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structure of TMD-TARPgamma2

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