3O21: GluA3 N-terminal domain

High resolution structure of GluA3 N-terminal domain (NTD). Determined by X-ray diffraction at 2.2 Å resolution. Released 9 Mar 2011.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 12,793
Mol. weight: 182.04 kDa
Ligands: NAG, PO4
Released: 9 Mar 2011

Explore 3O21 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3O21 contains 60 α-helices and 71 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.

Chain A: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	1
α-helix	17-31	15
β-strand	42-49	8	1
α-helix	55-66	12
β-strand	73-75	3	1
α-helix	82-92	11
β-strand	96-98	3	1
α-helix	101-103	3
β-strand	110-112	3	1
α-helix	115-116	2
α-helix	118-128	11
β-strand	132-137	6	2
α-helix	144-155	12
β-strand	159-164	6	2
α-helix	172-182	11
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	277-298	22
α-helix	324-331	8
β-strand	335-337	3	3
β-strand	340-342	3	3
β-strand	344	1	4
β-strand	349	1	1
β-strand	350	1	4
β-strand	355-361	7	2
β-strand	364-372	9	2
β-strand	376-378	3	2

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	5
α-helix	17-31	15
β-strand	42-49	8	5
α-helix	55-68	14
β-strand	73-75	3	5
α-helix	82-91	10
β-strand	96-98	3	5
α-helix	101-103	3
β-strand	110-112	3	5
α-helix	115-116	2
α-helix	118-128	11
β-strand	132-137	6	6
α-helix	144-155	12
β-strand	159-164	6	6
α-helix	172-183	12
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	323-332	10
β-strand	335-337	3	7
β-strand	340-342	3	7
β-strand	344	1	8
β-strand	349	1	5
β-strand	350	1	8
β-strand	355-361	7	6
β-strand	364-372	9	6
β-strand	376-379	4	6

Chain C: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	9
α-helix	17-31	15
β-strand	42-49	8	9
α-helix	55-68	14
β-strand	73-75	3	9
α-helix	82-92	11
α-helix	94-95	2
β-strand	96-98	3	9
α-helix	101-103	3
β-strand	110-112	3	9
α-helix	115-116	2
α-helix	118-128	11
β-strand	132-137	6	10
α-helix	144-156	13
β-strand	159-164	6	10
α-helix	171-182	12
β-strand	188-192	5	10
α-helix	195-208	14
β-strand	216-219	4	10
α-helix	224-226	3
α-helix	230-233	4
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	11
β-strand	340-342	3	11
β-strand	343-344	2	12
β-strand	350-351	2	12
β-strand	355-361	7	10
β-strand	364-372	9	10
β-strand	376-379	4	10

Chain D: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	13
α-helix	17-32	16
β-strand	42-49	8	13
α-helix	55-67	13
β-strand	73-75	3	13
α-helix	82-91	10
β-strand	96-98	3	13
α-helix	101-103	3
β-strand	110-112	3	13
α-helix	115-116	2
α-helix	118-128	11
β-strand	132-137	6	14
α-helix	144-155	12
β-strand	159-164	6	14
α-helix	171-182	12
β-strand	188-192	5	14
α-helix	195-208	14
β-strand	216-219	4	14
α-helix	224-226	3
α-helix	230-233	4
β-strand	238-243	6	14
α-helix	250-259	10
α-helix	274-276	3
α-helix	277-298	22
α-helix	322-332	11
β-strand	335-337	3	15
β-strand	340-342	3	15
β-strand	344	1	16
β-strand	349	1	13
β-strand	350	1	16
β-strand	355-361	7	14
β-strand	364-372	9	14
β-strand	376-379	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 3	A, B, C, D	protein	389	Rattus norvegicus	P19492 (AlphaFold model)

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

>3O21_1 Glutamate receptor 3 (chains A, B, C, D)
GFPNTISIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTN
AFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFVTPSFPTDADVQFVIQMRPALKGA
ILSLLSYYKWEKFVYLYDTERGFSVLQAIMEAAVQNNWQVTARSVGNIKDVQEFRRIIEE
MDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDILLERVMHGGANIT
GFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIAEAFRYLRRQR
VDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEM
KVSGSRKAGYWNEYERFVPFSGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
PO4	Phosphate ion	O4 P	2

Primary citation

Dynamics and allosteric potential of the AMPA receptor N-terminal domain. Sukumaran, M., Rossmann, M., Shrivastava, I. et al. EMBO J (2011) 30:972-982. DOI 10.1038/emboj.2011.17 · 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
6FPJ 1.96 Å, Structure of the AMPAR GluA3 N-terminal domain bound to phosphate
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

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