7TNM: Complex GNGN2 of AMPA-subtype iGluR GluA2

Complex GNGN2 of AMPA-subtype iGluR GluA2 in complex with auxiliary subunit gamma2 (Stargazin) at low glutamate concentration (20 uM) in the presence of cyclothiazide (100 uM). Determined by electron microscopy at 4.74 Å resolution. Released 20 Apr 2022.

Method: Electron microscopy
Resolution: 4.74 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 19,448
Mol. weight: 463.63 kDa
Ligands: GLU, CYZ
Released: 20 Apr 2022

Explore 7TNM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TNM contains 110 α-helices and 104 β-strands across 4 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: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	395-399	5	1
β-strand	407-408	2	2
α-helix	417-420	4
β-strand	421-422	2	2
α-helix	424-436	13
β-strand	440-444	5	1
β-strand	453	1	3
α-helix	454	1
β-strand	460	1	3
α-helix	462-469	8
β-strand	474-475	2	1
β-strand	480	1	1
α-helix	483-488	6
β-strand	489-498	10	1
β-strand	500-505	6	4
α-helix	506-508	3
α-helix	516-518	3
β-strand	521	1	5
α-helix	523-544	22
α-helix	565-568	4
α-helix	573-584	12
α-helix	596-624	29
α-helix	636-641	6
β-strand	646	1	6
β-strand	650	1	7
α-helix	654-661	8
α-helix	665-675	11
β-strand	683	1	7
α-helix	686-695	10
β-strand	700	1	6
β-strand	702-705	4	4
α-helix	706-713	8
β-strand	720-722	3	4
β-strand	730-737	8	1
α-helix	743-755	13
α-helix	758-769	12
β-strand	787	1	8
α-helix	793-819	27
α-helix	1005-1027	23
β-strand	1033-1035	3	9
β-strand	1058-1060	3	9
β-strand	1064	1	10
β-strand	1067	1	9
β-strand	1078	1	10
α-helix	1092-1102	11
α-helix	1105-1122	18
α-helix	1133-1160	28
β-strand	1174-1175	2	9
α-helix	1177-1208	32

Chains B and D: 31 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	395-399	5	11
β-strand	407-408	2	12
α-helix	417-419	3
β-strand	421-422	2	12
α-helix	424-436	13
β-strand	440-444	5	11
β-strand	452-453	2	13
β-strand	460-461	2	13
α-helix	463-468	6
β-strand	474	1	11
β-strand	475	1	14
β-strand	480	1	15
α-helix	483-488	6
α-helix	490	1
β-strand	491	1	14
α-helix	492-494	3
β-strand	496-499	4	15
β-strand	500-505	6	16
α-helix	506-508	3
α-helix	516-518	3
β-strand	521	1	17
α-helix	523-544	22
α-helix	564-567	4
α-helix	573-584	12
α-helix	596-616	21
α-helix	621-623	3
α-helix	636-640	5
β-strand	646-648	3	16
β-strand	649-650	2	18
α-helix	654-661	8
α-helix	665-675	11
β-strand	682-683	2	18
α-helix	686-696	11
β-strand	700-705	6	16
α-helix	706-714	9
β-strand	720-723	4	16
β-strand	729-732	4	15
β-strand	735	1	14
α-helix	743-755	13
α-helix	758-768	11
α-helix	776-779	4
α-helix	786	1
β-strand	787	1	5
α-helix	788	1
α-helix	790-792	3
α-helix	793-818	26
α-helix	1005-1028	24
β-strand	1033-1037	5	19
α-helix	1040-1042	3
β-strand	1056-1060	5	19
β-strand	1064-1066	3	20
β-strand	1067	1	19
β-strand	1076-1078	3	20
α-helix	1092-1102	11
α-helix	1105-1122	18
α-helix	1133-1158	26
β-strand	1174-1175	2	19
α-helix	1177-1208	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-3 subunit chimera	A, B, C, D	protein	1033	Rattus norvegicus	P19491 (AlphaFold model), Q8VHX0 (AlphaFold model)

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

>7TNM_1 Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-3 subunit chimera (chains A, B, C, D)
NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRG
VYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQ
WDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKE
RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVD
YDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPR
KIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLA
AEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVI
DFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPY
EWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFT
LIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDK
MWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDS
KGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGAKDSGSKEKTSALSL
SNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKGTGLFDRGVQMLLTTVGAFAAFS
LMTIAVGTDYWLYSRGVCKTKSVSEDETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDH
FPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFF
VSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFI
DRHKQLTGGLVPR

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2
CYZ	Cyclothiazide	C14 H16 Cl N3 O4 S2	4

Primary citation

Opening of glutamate receptor channel to subconductance levels. Yelshanskaya, M.V., Patel, D.S., Kottke, C.M. et al. Nature (2022) 605:172-178. DOI 10.1038/s41586-022-04637-w · 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…

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