6FPJ: AMPAR GluA3 N-terminal domain

Structure of the AMPAR GluA3 N-terminal domain bound to phosphate. Determined by X-ray diffraction at 1.96 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 10,060
Mol. weight: 138.36 kDa
Ligands: PO4, NAG
Released: 19 Dec 2018

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

Secondary structure: helices and β-sheets

6FPJ contains 45 α-helices and 56 β-strands across 3 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: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	1
α-helix	17-31	15
β-strand	42-50	9	1
α-helix	55-68	14
β-strand	73-75	3	1
α-helix	82-91	10
β-strand	96-98	3	1
α-helix	101-102	2
β-strand	110-112	3	1
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	2
α-helix	144-156	13
β-strand	159-164	6	2
α-helix	171-183	13
β-strand	188-192	5	2
α-helix	195-208	14
β-strand	216-219	4	2
α-helix	224-226	3
α-helix	230-234	5
β-strand	238-243	6	2
α-helix	250-259	10
α-helix	274-276	3
α-helix	277-298	22
α-helix	323-331	9
β-strand	335-337	3	3
β-strand	340-342	3	3
β-strand	343-344	2	4
β-strand	349	1	1
β-strand	350-351	2	4
β-strand	355-361	7	2
β-strand	364-372	9	2
β-strand	376-379	4	2

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	5
α-helix	17-31	15
β-strand	42-50	9	5
α-helix	55-68	14
β-strand	73-75	3	5
α-helix	82-92	11
β-strand	96-98	3	5
α-helix	101-103	3
β-strand	110-112	3	5
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	6
α-helix	144-156	13
β-strand	159-164	6	6
α-helix	171-183	13
β-strand	188-192	5	6
α-helix	195-208	14
β-strand	216-219	4	6
α-helix	224-226	3
α-helix	230-234	5
β-strand	238-243	6	6
α-helix	250-259	10
α-helix	274-276	3
α-helix	277-298	22
α-helix	323-331	9
β-strand	335-337	3	7
β-strand	340-342	3	7
β-strand	343-344	2	8
β-strand	349	1	5
β-strand	350-351	2	8
β-strand	354-361	8	6
β-strand	364-372	9	6
β-strand	376-379	4	6

Chain C: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	9
α-helix	17-31	15
β-strand	42-50	9	9
α-helix	55-68	14
β-strand	73-75	3	9
α-helix	82-91	10
β-strand	96-98	3	9
α-helix	101-102	2
β-strand	110-112	3	9
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	10
α-helix	144-152	9
β-strand	159-164	6	10
α-helix	171-183	13
β-strand	188-192	5	10
α-helix	195-207	13
β-strand	212	1	11
β-strand	216-219	4	10
α-helix	224-226	3
α-helix	230-235	6
β-strand	236	1	11
β-strand	238-243	6	10
α-helix	250-259	10
α-helix	274-276	3
α-helix	277-298	22
α-helix	322-331	10
β-strand	335-337	3	12
β-strand	340-342	3	12
β-strand	343-344	2	13
β-strand	349	1	9
β-strand	350-351	2	13
β-strand	354-359	6	10
β-strand	366-372	7	10
β-strand	376-379	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 3	A, B, C	protein	390	Rattus norvegicus	P19492 (AlphaFold model)

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

>6FPJ_1 Glutamate receptor 3 (chains A, B, C)
GFPNTISIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTN
AFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFVTPSFPTDADVQFVIQMRPALKGA
ILSLLSYYKWEKFVYLYDTERGFSVLQAIMEAAVQNNWQVTARSVGNIKDVQEFRRIIEE
MDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDILLERVMHGGANIT
GFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIAEAFRYLRRQR
VDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEM
KVSGSRKAGYWNEYERFVPFSGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	7
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (GOL, DMS) are not listed.

Primary citation

Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain. Lee, J.Y., Krieger, J., Herguedas, B. et al. Structure (2019) 27:241-252.e3. DOI 10.1016/j.str.2018.10.017 · PubMed

Other PDB entries of the same protein (UniProt P19492 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4F29 1.75 Å, Quisqualate bound to the ligand binding domain of GluA3i
3LSW 1.75 Å, Aniracetam bound to the ligand binding domain of GluA3
4F1Y 1.79 Å, CNQX bound to the ligand binding domain of GluA3
3M3K 1.79 Å, Ligand binding domain (S1S2) of GluA3 (flop)
4F3B 1.82 Å, Glutamate bound to the D655A mutant of the ligand binding domain of GluA3
4F39 1.83 Å, Kainate bound to the ligand binding domain of GluA3
3DLN 1.91 Å, Crystal structure of the binding domain of the AMPA subunit GluR3 bound to glutamate
4F2O 1.91 Å, Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3
3LSX 2.01 Å, Piracetam bound to the ligand binding domain of GluA3
4F22 2.06 Å, Kainate bound to the K660A mutant of the ligand binding domain of GluA3
4F3G 2.06 Å, Kainate bound to the ligand binding domain of GluA3i
3DP4 2.11 Å, Crystal structure of the binding domain of the AMPA subunit GluR3 bound to AMPA

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