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4f31

Kainate bound to the D655A mutant of the ligand binding domain of GluA3

Method: X-RAY DIFFRACTION Dmax: 79.6 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 B； UniProt 417–530 Chain B； UniProt 658–799 Chain D； UniProt 417–530 Chain D； UniProt 658–799 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

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 4F31 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 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 mutation/modification Different ligand/ion 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 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 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 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
4F39 Kainate bound to the ligand binding domain of GluA3 Deposited 2012-05-09 Different construct Different mutation/modification Different ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 B； PDBConstruct 1–114； UniProt 417–530 Author chain B； PDBConstruct 117–258； UniProt 658–799 Author chain D； PDBConstruct 1–114； UniProt 417–530 Author chain D； 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

SAXS profile for 4f31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f31
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f31
Deposition date deposition_date2012-05-08
Structure title titleKainate bound to the D655A mutant of the ligand binding domain of GluA3
Keywords keywordsglutamate receptor, GluA3, GluR3, AMPA receptor, S1S2, LBD, neurotransmitter receptor, Kainate, TRANSPORT PROTEIN-AGONIST complex; TRANSPORT PROTEIN/AGONIST
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.47 Å
Radius of gyration Rg (electron density) rg_electron24.25 Å
Forward intensity I(0) i053606100.00
Molecular weight molecular_weight58205.0 kDa
Excluded volume excluded_volume73509 ų
Envelope volume envelope_volume88997 ų
Hydration-shell volume shell_volume29832 ų
Envelope diameter envelope_diameter86.2 Å
Shell Rg shell_rg32.18 Å
Envelope Rg envelope_rg24.43 Å
Shape Rg shape_rg24.22 Å
Total Rg total_rg25.30 Å
Total atoms total_atoms4076
Residues n_residues516
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.6 Å
Rg (real space) rg_real25.34 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real5.3610e+07
I(0) uncertainty (real space) i0_real_error8.3270e+05
Rg (reciprocal space) rg_reciprocal25.38 Å
I(0) (reciprocal space) i0_reciprocal53610000.0000
Solution quality estimate total_estimate0.8264
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary70.6 Å
Skewness Skewness skewness0.154
Kurtosis Kurtosis kurtosis-0.483
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13250000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4f31b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd4f31d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id4f31B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4f31B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4f31D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id4f31D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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8. Citations (1)

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9. Files and Curves (10)