8P3Y: Glutamate receptor 2

Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 3. Determined by electron microscopy at 3.55 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 17,012
Mol. weight: 538.38 kDa
Released: 30 Aug 2023

Explore 8P3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P3Y contains 104 α-helices and 109 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	394-399	6	1
β-strand	407-408	2	2
α-helix	409	1
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	2
α-helix	424-436	13
β-strand	439-444	6	1
β-strand	451-453	3	3
β-strand	460-461	2	3
α-helix	462-468	7
β-strand	474	1	1
β-strand	475	1	4
α-helix	479	1
β-strand	480	1	5
α-helix	481	1
α-helix	483-488	6
β-strand	489-491	3	4
β-strand	496-499	4	5
β-strand	500-505	6	6
α-helix	516-518	3
β-strand	521	1	7
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-623	28
α-helix	636-641	6
β-strand	646-648	3	6
β-strand	650	1	8
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	8
α-helix	686-694	9
β-strand	700-705	6	6
α-helix	706-713	8
β-strand	720-723	4	6
β-strand	729-732	4	5
β-strand	735-737	3	4
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
β-strand	787	1	9
α-helix	789-819	31

Chain B: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	394-399	6	10
β-strand	407-408	2	11
α-helix	412-414	3
β-strand	421-422	2	11
α-helix	424-436	13
β-strand	439-444	6	10
β-strand	451-453	3	12
β-strand	460-461	2	12
α-helix	462-468	7
β-strand	474	1	10
β-strand	475	1	13
α-helix	479	1
β-strand	480	1	14
α-helix	481	1
α-helix	483-488	6
β-strand	489-491	3	13
β-strand	496-499	4	14
β-strand	500-505	6	15
α-helix	516-518	3
β-strand	521	1	16
α-helix	523-545	23
α-helix	573-584	12
α-helix	596-623	28
α-helix	636-641	6
β-strand	646-648	3	15
β-strand	650	1	17
α-helix	654-660	7
α-helix	665-676	12
β-strand	683	1	17
α-helix	686-694	9
β-strand	700-705	6	15
α-helix	706-713	8
β-strand	720-723	4	15
β-strand	729-732	4	14
β-strand	735-737	3	13
α-helix	743-756	14
α-helix	758-767	10
α-helix	768-770	3
α-helix	785-786	2
β-strand	787	1	7
α-helix	788	1
α-helix	793-822	30

Chain C: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	394-399	6	18
β-strand	407-408	2	19
α-helix	409	1
α-helix	412-414	3
β-strand	421-422	2	19
α-helix	424-436	13
β-strand	439-444	6	18
β-strand	453-454	2	20
β-strand	459-460	2	20
α-helix	462-469	8
β-strand	474	1	18
β-strand	480-481	2	21
α-helix	483-488	6
β-strand	490-491	2	22
β-strand	496-499	4	21
β-strand	500-504	5	23
α-helix	516-518	3
β-strand	521	1	24
α-helix	523-545	23
α-helix	548-550	3
α-helix	573-584	12
α-helix	596-619	24
α-helix	636-641	6
β-strand	646-648	3	23
β-strand	650	1	25
α-helix	654-660	7
α-helix	665-676	12
β-strand	683	1	25
α-helix	686-694	9
β-strand	700-705	6	23
α-helix	706-713	8
β-strand	721-723	3	23
β-strand	729-732	4	21
β-strand	735-736	2	22
α-helix	743-756	14
α-helix	758-767	10
α-helix	786	1
β-strand	787	1	16
α-helix	788	1
α-helix	793-820	28

Chain D: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	394-399	6	26
β-strand	407-408	2	27
α-helix	412-414	3
α-helix	418-420	3
β-strand	421-422	2	27
α-helix	424-436	13
β-strand	439-444	6	26
β-strand	453	1	28
β-strand	460	1	28
α-helix	462-468	7
β-strand	474	1	26
β-strand	475	1	29
α-helix	479	1
β-strand	480	1	30
α-helix	481	1
α-helix	483-488	6
β-strand	489-491	3	29
β-strand	496-499	4	30
β-strand	500-505	6	31
β-strand	510	1	32
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	625-628	4
β-strand	630	1	32
α-helix	636-641	6
β-strand	646-649	4	31
β-strand	650	1	33
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	33
α-helix	686-694	9
β-strand	700-705	6	31
α-helix	706-713	8
β-strand	720-723	4	31
β-strand	729-732	4	30
β-strand	735-737	3	29
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
β-strand	787	1	24
α-helix	789-822	34

Chain E: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-29	22
β-strand	34-38	5	34
β-strand	57-61	5	34
β-strand	67-68	2	34
α-helix	93-103	11
α-helix	106-123	18
α-helix	134-159	26
β-strand	176	1	34
α-helix	178-209	32

Chain F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-27	22
β-strand	34-35	2	35
β-strand	37-38	2	36
β-strand	57-58	2	36
β-strand	59	1	37
β-strand	65-67	3	38
β-strand	68	1	37
β-strand	77-79	3	38
α-helix	93-103	11
α-helix	106-126	21
α-helix	134-159	26
β-strand	175-176	2	35
α-helix	178-208	31

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-29	22
β-strand	34-38	5	39
β-strand	57-61	5	39
β-strand	65-68	4	39
β-strand	77-79	3	39
α-helix	93-103	11
α-helix	106-126	21
α-helix	134-160	27
β-strand	174-176	3	39
α-helix	178-209	32

Chain H: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34	1	40
β-strand	36-38	3	41
β-strand	57-59	3	41
β-strand	65-67	3	42
β-strand	68	1	41
β-strand	77-79	3	42
α-helix	94-103	10
α-helix	106-123	18
α-helix	134-160	27
β-strand	176	1	40
α-helix	178-208	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 2	A, B, C, D	protein	881	Rattus norvegicus	P19491 (AlphaFold model)
Voltage-dependent calcium channel gamma-2 subunit	E, F, G, H	protein	323	Rattus norvegicus	Q71RJ2 (AlphaFold model)

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

>8P3Y_1 Glutamate receptor 2 (chains A, B, C, D)
MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTP
HIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFIGFPTDGTH
PFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGN
INNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGF
TDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYD
AVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKF
DQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTTIL
ESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWN
GMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPL
AYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSL
GAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSK
QTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYA
YLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVLDK
LKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAE
AKRMKVAKNPQNINPSSSQNSQNFATYKEGYNVYGIESVKI

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

>8P3Y_2 Voltage-dependent calcium channel gamma-2 subunit (chains E, F, G, H)
MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTH
SGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGL
CIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSF
YFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSS
SRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVH
NCIQKDSKDSLHANTANRRTTPV

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 P19491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YK4 1.0 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5NG9 1.15 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
6YK5 1.15 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
6YK3 1.2 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5JEI 1.23 Å, Crystal structure of the GluA2 LBD in complex with FW
4IGT 1.24 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist…
4YU0 1.26 Å, Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with…
5NIH 1.3 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
1MQI 1.35 Å, Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with…
5FTI 1.35 Å, Crystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
4U21 1.39 Å, GluA2flip sLBD complexed with FW and (R,R)-2b crystal form E
4FAT 1.4 Å, Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an…

Browse structure collections

About this viewer

MolViewer shows 8P3Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.