3p3w

Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution

Method: X-RAY DIFFRACTION D_max: 134.5 Å Quality: GOOD

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

Glutamate receptor 3

Rattus norvegicus

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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–403 Chain C； UniProt 23–403	Fragment：N-terminal domain	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 23–403 Chain D； UniProt 23–403	Fragment：N-terminal domain	No other associated polymer	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

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 3P3W	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 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
3LSX Piracetam bound to the ligand binding domain of GluA3 Deposited 2010-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 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
3M3F PEPA bound to the ligand binding domain of GluA3 (flop form) Deposited 2010-03-09	Different construct 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 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 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 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 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
3RT6 Fluorowillardiine bound to the ligand binding domain of GluA3 Deposited 2011-05-03	Different construct 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 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 oligomeric state 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 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 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 mutation/modification 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 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 mutation/modification 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 37 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 1–381； UniProt 23–403 Author chain B； PDBConstruct 1–381； UniProt 23–403 Author chain C； PDBConstruct 1–381； UniProt 23–403 Author chain D； PDBConstruct 1–381； UniProt 23–403

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	3p3w
Deposition date deposition_date	2010-10-05
Structure title title	Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution
Keywords keywords	Periplasmatic binding protein, 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	39.84 Å
Radius of gyration Rg (electron density) rg_electron	39.34 Å
Forward intensity I(0) i0	401947000.00
Molecular weight molecular_weight	162710.0 kDa
Excluded volume excluded_volume	203060 Å³
Envelope volume envelope_volume	281560 Å³
Hydration-shell volume shell_volume	60063 Å³
Envelope diameter envelope_diameter	139.1 Å
Shell Rg shell_rg	44.60 Å
Envelope Rg envelope_rg	38.65 Å
Shape Rg shape_rg	39.36 Å
Total Rg total_rg	39.60 Å
Total atoms total_atoms	11484
Residues n_residues	1482
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	134.5 Å
Rg (real space) rg_real	39.88 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	4.0190e+08
I(0) uncertainty (real space) i0_real_error	7.3740e+06
Rg (reciprocal space) rg_reciprocal	39.86 Å
I(0) (reciprocal space) i0_reciprocal	401900000.0000
Solution quality estimate total_estimate	0.8646
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.4 Å
Skewness Skewness skewness	0.405
Kurtosis Kurtosis kurtosis	-0.173
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	130600000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.789

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	110.960 Å
Unit-cell length b length_b	127.920 Å
Unit-cell length c length_c	130.050 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	55.410 Å
R factor r_factor	0.3075
R_work r_work	0.3059
R_free r_free	0.3377

Description description	Glutamate receptor 3
Molecular weight formula_weight	44964.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11484

Structure of a dimeric GluA3 N-terminal domain (NTD) at 4.2 A resolution

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

Glutamate receptor 3

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

fit	/app/data/saxs_computation/p3/3p3w/3p3w.fit
pddf	/app/data/pr_computation/p3/3p3w/3p3w.pr.out
profile	/app/data/saxs_computation/p3/3p3w/3p3w.dat