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3kfm

Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate

Method: X-RAY DIFFRACTION Dmax: 62.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor 4

Rattus norvegicus

UniProt P19493

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 416–528 Chain A； UniProt 654–795 Fragment：ligand binding domain Mutation：L134V KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；291 K；18% PEG 8000, 0.1M Na-Acetate, 0.2M Ammonium Sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.20 Å R-free 0.274

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 3KFM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EN3 Crystal Structure of the GluR4 Ligand-Binding domain in complex with kainate Deposited 2008-09-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 416–528（113 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Chain A 654–795（142 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Not recorded KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；25.5% PEG 1500, 0.05M Na-Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.43 Å R-free 0.219
3EN3 Crystal Structure of the GluR4 Ligand-Binding domain in complex with kainate Deposited 2008-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 416–528（113 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Chain A 654–795（142 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Not recorded KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；25.5% PEG 1500, 0.05M Na-Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.43 Å R-free 0.219
3EPE Crystal Structure of the GluR4 Ligand-Binding domain in complex with glutamate Deposited 2008-09-29 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 416–528（113 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Chain A 654–795（142 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Chain B 416–528（113 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Chain B 654–795（142 aa） Fragment：ligand binding domain (UNP residues 416-528 and 654-958)
Not recorded GLU GLUTAMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；25% PEG 4000, 0.1M Na-Acetate pH 4.6, 0.2M Ammonium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.220
3FAS X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-glutamate at 1.40A resolution Deposited 2008-11-18 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 415–528（114 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain A 654–796（143 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain B 415–528（114 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain B 654–796（143 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Not recorded GLU GLUTAMIC ACID × 2 SO4 SULFATE ION × 8 GOL GLYCEROL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；280 K；PEG4000, Acetate, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 1.40 Å R-free 0.183
3FAT X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution Deposited 2008-11-18 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 415–528（114 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain A 654–796（143 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain B 415–528（114 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain B 654–796（143 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Not recorded AMQ (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID × 2 SO4 SULFATE ION × 5 GOL GLYCEROL × 5 ACY ACETIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；280 K；PEG 4000, Acetate, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 1.90 Å R-free 0.216
3FAT X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution Deposited 2008-11-18 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 415–528（114 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Chain C 654–796（143 aa） Fragment：iGluR4 flip ligand-binding core (S1S2)
Not recorded AMQ (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID × 2 SO4 SULFATE ION × 4 GOL GLYCEROL × 8 ACY ACETIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；280 K；PEG 4000, Acetate, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 1.90 Å R-free 0.216
3KEI Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with glutamate Deposited 2009-10-26 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 416–528（113 aa） Fragment：ligand binding domain
Chain A 654–795（142 aa） Fragment：ligand binding domain
Chain B 416–528（113 aa） Fragment：ligand binding domain
Chain B 654–795（142 aa） Fragment：ligand binding domain
Mutation：L134V Mutation：L134V Mutation：L134V Mutation：L134V GLU GLUTAMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；24% PEG 4000, 0.1M Na-Acetate, 0.3M Ammonium Sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.224
4GPA High resolution structure of the GluA4 N-terminal domain (NTD) Deposited 2012-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 22–401（380 aa） Fragment：N-terminal domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.74M sodium citrate, 0.1M cacodylate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Resolution 2.25 Å R-free 0.235
5FWX Crystal structure of the AMPA receptor GluA2/A4 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 22–401（380 aa） Fragment：RESIDUES 22-401
Not recorded SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 17% PEG 3350 WITH 0.1-0.35 M AMMONIUM SULPHATE
Resolution 2.50 Å R-free 0.238
5FWX Crystal structure of the AMPA receptor GluA2/A4 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 22–401（380 aa） Fragment：RESIDUES 22-401
Not recorded SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 17% PEG 3350 WITH 0.1-0.35 M AMMONIUM SULPHATE
Resolution 2.50 Å R-free 0.238
9IGZ GluA4 in complex with TARP-2, resting state, structure of N-terminal domain Deposited 2025-02-20 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 × 4 PDB declaration: tetrameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9NR6 The structure of Noelin 1 with cerebellar GluA1/A4-ATD Deposited 2025-03-14 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 × 8 PDB declaration: octameric
Chain B 22–399（378 aa）
Chain D 22–399（378 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9NR7 The structure of GluA1/A4 LBD-TMD in Noelin-AMPAR complex Deposited 2025-03-14 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 × 8 PDB declaration: octameric
Chain B 417–840（424 aa）
Chain D 417–840（424 aa）
Not recorded ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9NR8 The structure of cerebellar GluA1/A4 ATD Deposited 2025-03-14 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 × 6 PDB declaration: hexameric
Chain B 22–399（378 aa）
Chain D 22–399（378 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
9NR9 The structure of GluA1/A4 LBD-TMD with 2 TARPs Deposited 2025-03-14 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 × 6 PDB declaration: hexameric
Chain B 417–840（424 aa）
Chain D 417–840（424 aa）
Not recorded ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
9NRA The structure of GluA1/A4 LBD-TMD with 4 auxiliary subunits Deposited 2025-03-14 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 × 8 PDB declaration: octameric
Chain B 417–840（424 aa）
Chain D 417–840（424 aa）
Not recorded ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9P9B Activated GluA4 homotetrameric AMPAR. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
9P9C Active substate 1 of the GluA4 homotetramer. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded CYZ CYCLOTHIAZIDE × 4 GLU GLUTAMIC ACID × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.01 Å
9P9D Active substate 2 of the GluA4 homotetramer. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9P9E Active substate 3 of the GluA4 homotetramer. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9P9F Active substate 4 of the GluA4 homotetramer. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.89 Å
9P9G Active substate 5 of the GluA4 homotetramer. Deposited 2025-06-24 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 × 8 PDB declaration: octameric
Chain A 25–848（824 aa）
Chain B 25–848（824 aa）
Chain C 25–848（824 aa）
Chain D 25–848（824 aa）
Not recorded GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.06 Å
9QDN GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD Deposited 2025-03-06 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 × 8 PDB declaration: octameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded PLM PALMITIC ACID × 16 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 E2Q 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
9QPW GluA4, resting state, structure of TMD/LBD Deposited 2025-03-29 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 × 4 PDB declaration: tetrameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded E2Q 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9RMS GluA4 in complex with TARP-2, Resting II state, structure of TMD/LBD domains Deposited 2025-06-18 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 × 8 PDB declaration: octameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded E2Q 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9RMW GluA4 in complex with TARP-2, open state, structure of TMD/LBD domains Deposited 2025-06-18 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 × 8 PDB declaration: octameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded PLM PALMITIC ACID × 18 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 CYZ CYCLOTHIAZIDE × 4 GLU GLUTAMIC ACID × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9RN4 GluA4 in complex with TARP-2, desensitized state, structure of TMD/LBD domains Deposited 2025-06-19 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 × 8 PDB declaration: octameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded PLM PALMITIC ACID × 4 CA CALCIUM ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9RN7 GluA4 in complex with TARP-2, Desensitized state, structure of TMD domain Deposited 2025-06-19 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 × 8 PDB declaration: octameric
Chain A 21–902（882 aa）
Chain B 21–902（882 aa）
Chain C 21–902（882 aa）
Chain D 21–902（882 aa）
Not recorded PLM PALMITIC ACID × 4 CA CALCIUM ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

25 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRIA4_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–113； UniProt 416–528 Author chain A； PDBConstruct 116–257； UniProt 654–795

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 3kfm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kfm
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kfm
Deposition date deposition_date2009-10-27
Structure title titleCrystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate
Keywords keywords;GluA4, AMPA receptor, ligand-gated ion channel, ligand-binding domain, L651V, kainate, Alternative splicing, Cell junction, Cell membrane, Glycoprotein, Ion transport, Ionic channel, Lipoprotein, Membrane, Palmitate, Postsynaptic cell membrane, Receptor, Synapse, Transmembrane, Transport, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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_guinier19.61 Å
Radius of gyration Rg (electron density) rg_electron18.60 Å
Forward intensity I(0) i014046600.00
Molecular weight molecular_weight28901.0 kDa
Excluded volume excluded_volume36554 ų
Envelope volume envelope_volume42189 ų
Hydration-shell volume shell_volume18906 ų
Envelope diameter envelope_diameter63.7 Å
Shell Rg shell_rg24.77 Å
Envelope Rg envelope_rg18.91 Å
Shape Rg shape_rg18.57 Å
Total Rg total_rg19.60 Å
Total atoms total_atoms2028
Residues n_residues257
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 dmax62.3 Å
Rg (real space) rg_real19.52 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.4050e+07
I(0) uncertainty (real space) i0_real_error1.8500e+05
Rg (reciprocal space) rg_reciprocal19.53 Å
I(0) (reciprocal space) i0_reciprocal14050000.0000
Solution quality estimate total_estimate0.8217
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.7 Å
Skewness Skewness skewness0.204
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.4050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3102000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 0.998; 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 (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3kfma_
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 (2 domains)

Domain ID domain_id3kfmA01
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_id3kfmA02
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)