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9bwj

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in an apo state

Method: ELECTRON MICROSCOPY Dmax: 129.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycine receptor subunit alpha-3

Homo sapiens

UniProt O75311

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 5 其他Polymer 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–464 Chain B； UniProt 1–464 Chain C； UniProt 1–464 Chain D； UniProt 1–464 Chain E； UniProt 1–464 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 10 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 35 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.21 Å

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 9BWJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5CFB Crystal Structure of Human Glycine Receptor alpha-3 Bound to Strychnine Deposited 2015-07-08 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 Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Not recorded SY9 STRYCHNINE × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；30-33% PEG-400, 200 mM magnesium chloride, 100 mM potassium chloride, 25 mM sodium citrate
Resolution 3.04 Å R-free 0.283
5TIN Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607 Deposited 2016-10-03 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 × 5 PDB declaration: pentameric
Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q 7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 ZN ZINC ION × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES
Resolution 2.61 Å R-free 0.214
5TIO Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607 Deposited 2016-10-03 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 × 5 PDB declaration: pentameric
Chain A 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain A 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain B 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain C 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain D 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 34–342（309 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Chain E 419–460（42 aa） Fragment：UNP residues 34-460, with 343-418 deleted
Not recorded 7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 ZN ZINC ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES
Resolution 3.25 Å R-free 0.254
5VDH Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607, Glycine, and Ivermectin Deposited 2017-04-03 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 × 5 PDB declaration: pentameric
Chain A 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain A 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain B 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain B 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain C 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain C 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain D 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain D 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain E 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain E 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Not recorded 7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 5 ZN ZINC ION × 5 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5
Resolution 2.85 Å R-free 0.236
5VDI Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607, Glycine, and Ivermectin Deposited 2017-04-03 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 × 5 PDB declaration: pentameric
Chain A 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain A 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain B 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain B 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain C 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain C 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain D 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain D 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain E 34–342（309 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Chain E 419–460（42 aa） Fragment：UNP residues 34-342, ATG linker, UNP residues 419-460
Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q Mutation：N38Q 7C6 (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one × 5 GLY GLYCINE × 5 IVM (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside × 5 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5
Resolution 3.10 Å R-free 0.256
9BOY Cryo-EM structure of human Glycine Receptor apha3-beta heteromer with glycine in nanodisc Deposited 2024-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 34–464（431 aa）
Chain B 34–464（431 aa）
Chain C 34–464（431 aa）
Chain D 34–464（431 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.81 Å
9BOZ Cryo-EM structure of human Glycine Receptor alpha3-beta heteromer in presence of glycine Deposited 2024-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 34–464（431 aa）
Chain B 34–464（431 aa）
Chain C 34–464（431 aa）
Chain D 34–464（431 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
9BP0 Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta with glycine Deposited 2024-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 34–464（431 aa）
Chain B 34–464（431 aa）
Chain C 34–464（431 aa）
Chain D 34–464（431 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
9BP7 Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta in presence of glycine and 2,6-DTBP Deposited 2024-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 34–464（431 aa）
Chain B 34–464（431 aa）
Chain C 34–464（431 aa）
Chain D 34–464（431 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GLY GLYCINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9BU2 Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a desensitized state Deposited 2024-05-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9BU3 Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in a desensitized state Deposited 2024-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9BVH Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in an apo state. Deposited 2024-05-20 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 20 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CLR CHOLESTEROL × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
9BVJ Homomeric alpha3 glycine receptor in the presence of 1 mM glycine in an desensitized state. Deposited 2024-05-20 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9BWB Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in a desensitized state Deposited 2024-05-21 Different ligand/ion Different experimental conditions Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.21 Å
9BWC Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an apo state Deposited 2024-05-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 25 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 5 GLY GLYCINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
9BWE Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an intermediate state Deposited 2024-05-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 30 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 GLY GLYCINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
9BWG Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in a desensitized state Deposited 2024-05-21 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 ZN ZINC ION × 10 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9BZP Homomeric alpha3 glycine receptor in the presence of 0.1 millimolar glycine and 1 micromolar zinc in a desensitized state Deposited 2024-05-24 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–464（464 aa）
Chain B 1–464（464 aa）
Chain C 1–464（464 aa）
Chain D 1–464（464 aa）
Chain E 1–464（464 aa）
Not recorded GLY GLYCINE × 5 ZN ZINC ION × 5 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 25 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLRA3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–464； UniProt 1–464 Author chain B； PDBConstruct 1–464； UniProt 1–464 Author chain C； PDBConstruct 1–464； UniProt 1–464 Author chain D； PDBConstruct 1–464； UniProt 1–464 Author chain E； PDBConstruct 1–464； UniProt 1–464

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 9bwj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bwj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9bwj
Deposition date deposition_date2024-05-21
Structure title titleHomomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in an apo state
Keywords keywordsGlycine, Ion Channel, Ligand-Gated, Pentameric, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.49 Å
Radius of gyration Rg (electron density) rg_electron39.10 Å
Forward intensity I(0) i0566587000.00
Molecular weight molecular_weight209130.0 kDa
Excluded volume excluded_volume267380 ų
Envelope volume envelope_volume344740 ų
Hydration-shell volume shell_volume71281 ų
Envelope diameter envelope_diameter131.1 Å
Shell Rg shell_rg46.54 Å
Envelope Rg envelope_rg38.92 Å
Shape Rg shape_rg39.14 Å
Total Rg total_rg39.41 Å
Total atoms total_atoms14690
Residues n_residues1730
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 dmax129.8 Å
Rg (real space) rg_real39.41 Å
Rg uncertainty (real space) rg_real_error0.96 Å
I(0) (real space) i0_real5.6660e+08
I(0) uncertainty (real space) i0_real_error9.6280e+06
Rg (reciprocal space) rg_reciprocal39.46 Å
I(0) (reciprocal space) i0_reciprocal566600000.0000
Solution quality estimate total_estimate0.6470
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.4 Å
Skewness Skewness skewness0.346
Kurtosis Kurtosis kurtosis-0.281
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha102800000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.998; Smooth: 0.881
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)