3lsx

Piracetam bound to the ligand binding domain of GluA3

Method: X-RAY DIFFRACTION D_max: 63.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

GluA3 S1S2 domain

MUS MUSCULUS

UniProt P19492

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 417–530	Not recorded	GLU GLUTAMIC ACID × 2 PZI 2-(2-oxopyrrolidin-1-yl)acetamide × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.01 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3LSX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DLN Crystal structure of the binding domain of the AMPA subunit GluR3 bound to glutamate Deposited 2008-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–530（115 aa） Fragment：S1S2 binding domain Chain A 658–800（143 aa） Fragment：S1S2 binding domain	Not recorded	ZN ZINC ION × 1 GLU GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；15% PEG 8000, 0.2 M Zn acetate, 0.1 M Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.91 Å R-free 0.235
3DP4 Crystal structure of the binding domain of the AMPA subunit GluR3 bound to AMPA Deposited 2008-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–530（115 aa） Fragment：S1S2 binding domain Chain A 658–800（143 aa） Fragment：S1S2 binding domain	Not recorded	ZN ZINC ION × 2 AMQ (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；277 K；15-17% PEG 1450, 0.2 M Zn acetate, 0.2 M Ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.11 Å R-free 0.260
3LSW Aniracetam bound to the ligand binding domain of GluA3 Deposited 2010-02-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa）	Not recorded	GLU GLUTAMIC ACID × 2 4MP 1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.217
3M3F PEPA bound to the ligand binding domain of GluA3 (flop form) Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Fragment：UNP residues 417-530, 658-799 Chain A 658–799（142 aa） Fragment：UNP residues 417-530, 658-799	Not recorded	GLU GLUTAMIC ACID × 2 P99 2-[2,6-difluoro-4-({2-[(phenylsulfonyl)amino]ethyl}sulfanyl)phenoxy]acetamide × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.285
3M3K Ligand binding domain (S1S2) of GluA3 (flop) Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Fragment：UNP residues 417-530, 658-799 Chain A 658–799（142 aa） Fragment：UNP residues 417-530, 658-799 Chain C 417–530（114 aa） Fragment：UNP residues 417-530, 658-799 Chain C 658–799（142 aa） Fragment：UNP residues 417-530, 658-799	Not recorded	GLU GLUTAMIC ACID × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8000, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.79 Å R-free 0.240
3M3K Ligand binding domain (S1S2) of GluA3 (flop) Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 417–530（114 aa） Fragment：UNP residues 417-530, 658-799 Chain E 658–799（142 aa） Fragment：UNP residues 417-530, 658-799	Not recorded	GLU GLUTAMIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8000, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.79 Å R-free 0.240
3O21 High resolution structure of GluA3 N-terminal domain (NTD) Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–403（381 aa） Fragment：N-terminal domain Chain B 23–403（381 aa） Fragment：N-terminal domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；18% PEG 3350, 230mM sodium dihydrogen phosphate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.20 Å R-free 0.258
3O21 High resolution structure of GluA3 N-terminal domain (NTD) Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 23–403（381 aa） Fragment：N-terminal domain Chain D 23–403（381 aa） Fragment：N-terminal domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；18% PEG 3350, 230mM sodium dihydrogen phosphate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.20 Å R-free 0.258
3P3W Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution Deposited 2010-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–403（381 aa） Fragment：N-terminal domain Chain C 23–403（381 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.7；293 K；200mM ammonium phosphate, 20% PEG3350, pH 4.7, VAPOR DIFFUSION, temperature 293K	Resolution 4.20 Å R-free 0.338
3P3W Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution Deposited 2010-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 23–403（381 aa） Fragment：N-terminal domain Chain D 23–403（381 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.7；293 K；200mM ammonium phosphate, 20% PEG3350, pH 4.7, VAPOR DIFFUSION, temperature 293K	Resolution 4.20 Å R-free 0.338
3RT6 Fluorowillardiine bound to the ligand binding domain of GluA3 Deposited 2011-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 417–530（114 aa） Fragment：SEE REMARK 999 Chain B 658–799（142 aa） Fragment：SEE REMARK 999	Not recorded	FWD 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG8000, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.84 Å R-free 0.255
3RT8 Chlorowillardiine bound to the ligand binding domain of GluA3 Deposited 2011-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Fragment：SEE REMARK 999 Chain A 658–799（142 aa） Fragment：SEE REMARK 999	Not recorded	CWD 3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG8000, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.43 Å R-free 0.278
4F1Y CNQX bound to the ligand binding domain of GluA3 Deposited 2012-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa） Chain C 417–530（114 aa） Chain C 658–799（142 aa）	Not recorded	CNI 7-nitro-2,3-dioxo-2,3-dihydroquinoxaline-6-carbonitrile × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.79 Å R-free 0.251
4F22 Kainate bound to the K660A mutant of the ligand binding domain of GluA3 Deposited 2012-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Mutation：K660A Mutation：K660A	KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.06 Å R-free 0.244
4F29 Quisqualate bound to the ligand binding domain of GluA3i Deposited 2012-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Not recorded	QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 1.75 Å R-free 0.240
4F2O Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3 Deposited 2012-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Mutation：D655A Mutation：D655A	QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.91 Å R-free 0.228
4F2O Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3 Deposited 2012-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Mutation：D655A Mutation：D655A	QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.91 Å R-free 0.228
4F2Q Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3 Deposited 2012-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Mutation：D655A Mutation：D655A	QUS (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.261
4F31 Kainate bound to the D655A mutant of the ligand binding domain of GluA3 Deposited 2012-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 417–530（114 aa） Chain B 658–799（142 aa） Chain D 417–530（114 aa） Chain D 658–799（142 aa）	Mutation：D655A Mutation：D655A Mutation：D655A Mutation：D655A	KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.29 Å R-free 0.248
4F39 Kainate bound to the ligand binding domain of GluA3 Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Not recorded	KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.83 Å R-free 0.225
4F3B Glutamate bound to the D655A mutant of the ligand binding domain of GluA3 Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Mutation：D655A Mutation：D655A	GLU GLUTAMIC ACID × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.82 Å R-free 0.238
4F3G Kainate bound to the ligand binding domain of GluA3i Deposited 2012-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 417–530（114 aa） Chain A 658–799（142 aa）	Not recorded	KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.06 Å R-free 0.245
5FWY Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain heterodimer Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–403（381 aa） Fragment：RESIDUES 23-403	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 14-16 % PEG 3350, 0.27 M AMMONIUM SULPHATE AND 0.1 M BICINE PH 9	Resolution 2.12 Å R-free 0.231
5FWY Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain heterodimer Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–403（381 aa） Fragment：RESIDUES 23-403	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 14-16 % PEG 3350, 0.27 M AMMONIUM SULPHATE AND 0.1 M BICINE PH 9	Resolution 2.12 Å R-free 0.231
5IDE Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model I) Deposited 2016-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–888（865 aa） Chain D 24–888（865 aa）	Mutation：R439G, R265C Mutation：R439G, R265C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM Tris pH 7.4, 0.25 % DDM, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE；Incubated for 1 minute, blotted for 3 seconds	Resolution 8.25 Å
5IDF Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model II) Deposited 2016-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–888（865 aa） Chain D 24–888（865 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM Tris pH 7.4, 0.25 % DDM, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE；Incubated for 1 minute, blotted for 3 seconds	Resolution 10.31 Å
6FLR Super-open structure of the AMPAR GluA3 N-terminal domain Deposited 2018-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–403（381 aa） Chain B 23–403（381 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；18% PEG3350 and 0.2 M ammonium citrate	Resolution 2.51 Å R-free 0.257
6FPJ Structure of the AMPAR GluA3 N-terminal domain bound to phosphate Deposited 2018-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–403（381 aa） Chain C 23–403（381 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PO4 PHOSPHATE ION × 2 DMS DIMETHYL SULFOXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Ammonium dihydrogen phosphate pH 4.6 PEG3350	Resolution 1.96 Å R-free 0.219
6FPJ Structure of the AMPAR GluA3 N-terminal domain bound to phosphate Deposited 2018-02-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 23–403（381 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PO4 PHOSPHATE ION × 10 DMS DIMETHYL SULFOXIDE × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Ammonium dihydrogen phosphate pH 4.6 PEG3350	Resolution 1.96 Å R-free 0.219
6NJM Architecture and subunit arrangement of native AMPA receptors Deposited 2019-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–888（888 aa） Chain C 1–888（888 aa）	Not recorded	ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
6NJN Architecture and subunit arrangement of native AMPA receptors Deposited 2019-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 1–888（888 aa）	Not recorded	ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
9HPC The TMD and the LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state. Deposited 2024-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 24–865（842 aa） Chain B 24–865（842 aa） Chain C 24–865（842 aa） Chain D 24–865（842 aa） Chain W 24–865（842 aa） Chain X 24–865（842 aa） Chain Y 24–865（842 aa） Chain Z 24–865（842 aa）	Mutation：R439G Mutation：R439G Mutation：R439G Mutation：R439G Mutation：R439G Mutation：R439G Mutation：R439G Mutation：R439G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9HPD The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the open state. Deposited 2024-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 24–865（842 aa） Chain C 24–865（842 aa）	Mutation：R439G Mutation：R439G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9HPE The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state Deposited 2024-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 24–865（842 aa） Chain C 24–865（842 aa）	Mutation：R439G Mutation：R439G	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9HPF The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the desensitised state. Deposited 2024-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–865（842 aa） Chain B 24–865（842 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
9HPG The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3(R439G,R163I)- TARP gamma2 in the apo state. Deposited 2024-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 24–865（842 aa） Chain C 24–865（842 aa）	Mutation：R439G,R163I Mutation：R439G,R163I	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9HPK Open state TMD-LBD of the GluA3(R439G) with TARP gamma2 Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 24–865（842 aa） Chain B 24–865（842 aa） Chain C 24–865（842 aa） Chain D 24–865（842 aa） Chain W 24–865（842 aa） Chain X 24–865（842 aa） Chain Y 24–865（842 aa） Chain Z 24–865（842 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9QFH The composite map of of the AMPAR complex GluA3- TARP gamma2 in the apo state. Deposited 2025-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 24–865（842 aa） Chain B 24–865（842 aa） Chain C 24–865（842 aa） Chain D 24–865（842 aa） Chain W 24–865（842 aa） Chain X 24–865（842 aa） Chain Y 24–865（842 aa） Chain Z 24–865（842 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

32 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GRIA3_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–114； UniProt 417–530

GluA3 S1S2 domain

MUS MUSCULUS

UniProt Q9Z2W9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 658–799	Not recorded	GLU GLUTAMIC ACID × 2 PZI 2-(2-oxopyrrolidin-1-yl)acetamide × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.01 Å R-free 0.222

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3LSX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LSW Aniracetam bound to the ligand binding domain of GluA3 Deposited 2010-02-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 658–799（142 aa）	Not recorded	GLU GLUTAMIC ACID × 2 4MP 1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.217

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GRIA3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 117–258； UniProt 658–799

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lsx
Deposition date deposition_date	2010-02-13
Structure title title	Piracetam bound to the ligand binding domain of GluA3
Keywords keywords	glutamate receptor, GluR3, GluA3, AMPA receptor, neurotransmitter receptor, S1S2, allosteric modulator, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.60 Å
Radius of gyration Rg (electron density) rg_electron	18.56 Å
Forward intensity I(0) i0	14397300.00
Molecular weight molecular_weight	29258.0 kDa
Excluded volume excluded_volume	36964 Å³
Envelope volume envelope_volume	42745 Å³
Hydration-shell volume shell_volume	19157 Å³
Envelope diameter envelope_diameter	65.3 Å
Shell Rg shell_rg	24.83 Å
Envelope Rg envelope_rg	18.87 Å
Shape Rg shape_rg	18.53 Å
Total Rg total_rg	19.58 Å
Total atoms total_atoms	2052
Residues n_residues	258
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.5 Å
Rg (real space) rg_real	19.50 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.4400e+07
I(0) uncertainty (real space) i0_real_error	1.8030e+05
Rg (reciprocal space) rg_reciprocal	19.51 Å
I(0) (reciprocal space) i0_reciprocal	14400000.0000
Solution quality estimate total_estimate	0.8113
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3311000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	GluA3 S1S2 domain
Molecular weight formula_weight	28956.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2423

RTIVVTTILESPYVMYKKNHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGTPVNLAVLKLSEQGILDKLKNKWWYDKGEC

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	RAT, MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-(2-oxopyrrolidin-1-yl)acetamide
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3lsxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	3lsxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3lsxA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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8. Citations (1)

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Unit-cell length a length_a	47.364 Å
Unit-cell length b length_b	47.655 Å
Unit-cell length c length_c	137.981 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	2.006 Å
Low-resolution limit resolution_low	45.044 Å
R factor r_factor	0.1736
R_work r_work	0.1684
R_free r_free	0.2221

fit	/app/data/saxs_computation/ls/3lsx/3lsx.fit
pddf	/app/data/pr_computation/ls/3lsx/3lsx.pr.out
profile	/app/data/saxs_computation/ls/3lsx/3lsx.dat

Piracetam bound to the ligand binding domain of GluA3

1. Protein Identity and Related Structures Protein Identity & Related Structures

GluA3 S1S2 domain

State in the Current Structure

Other States of the Same Protein in the Database

GluA3 S1S2 domain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)