2yoe

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with GABA and flurazepam

Method: X-RAY DIFFRACTION D_max: 161.9 Å Quality: GOOD

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

CYS-LOOP LIGAND-GATED ION CHANNEL

ERWINIA CHRYSANTHEMI

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain F； UniProt 11–316 Chain G； UniProt 11–316 Chain H； UniProt 11–316 Chain I； UniProt 11–316 Chain J； UniProt 11–316	Not recorded	ABU GAMMA-AMINO-BUTANOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.90 Å R-free 0.230
2	Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 11–316 Chain B； UniProt 11–316 Chain C； UniProt 11–316 Chain D； UniProt 11–316 Chain E； UniProt 11–316	Not recorded	ABU GAMMA-AMINO-BUTANOIC ACID × 1 FL7 Flurazepam × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.90 Å R-free 0.230

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 2YOE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VL0 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Deposited 2008-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–321（321 aa） Chain B 1–321（321 aa） Chain C 1–321（321 aa） Chain D 1–321（321 aa） Chain E 1–321（321 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；15 % PEG 4000, 200MM AMMONIUM SULFATE, 50 MM ADA PH 6.5	Resolution 3.30 Å R-free 0.274
2VL0 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Deposited 2008-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 1–321（321 aa） Chain G 1–321（321 aa） Chain H 1–321（321 aa） Chain I 1–321（321 aa） Chain J 1–321（321 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；15 % PEG 4000, 200MM AMMONIUM SULFATE, 50 MM ADA PH 6.5	Resolution 3.30 Å R-free 0.274
2YKS PENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A Deposited 2011-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–321（321 aa） Chain B 1–321（321 aa） Chain C 1–321（321 aa） Chain D 1–321（321 aa） Chain E 1–321（321 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；50MM ADA PH6.5, 200MM NALISO4, 10% (W/V) PEG4000	Resolution 3.30 Å R-free 0.265
2YKS PENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A Deposited 2011-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 1–321（321 aa） Chain G 1–321（321 aa） Chain H 1–321（321 aa） Chain I 1–321（321 aa） Chain J 1–321（321 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；50MM ADA PH6.5, 200MM NALISO4, 10% (W/V) PEG4000	Resolution 3.30 Å R-free 0.265
3ZKR X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoform Deposited 2013-01-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 11–316（306 aa） Chain G 11–316（306 aa） Chain H 11–316（306 aa） Chain I 11–316（306 aa） Chain J 11–316（306 aa）	Not recorded	MBR TRIBROMOMETHANE × 11	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
3ZKR X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoform Deposited 2013-01-24	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–316（306 aa） Chain B 11–316（306 aa） Chain C 11–316（306 aa） Chain D 11–316（306 aa） Chain E 11–316（306 aa）	Not recorded	MBR TRIBROMOMETHANE × 11	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.65 Å R-free 0.264
4A97 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with zopiclone Deposited 2011-11-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–316（306 aa） Fragment：RESIDUES 11-316 Chain B 11–316（306 aa） Fragment：RESIDUES 11-316 Chain C 11–316（306 aa） Fragment：RESIDUES 11-316 Chain D 11–316（306 aa） Fragment：RESIDUES 11-316 Chain E 11–316（306 aa） Fragment：RESIDUES 11-316	Not recorded	ZPC (5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.34 Å R-free 0.259
4A97 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with zopiclone Deposited 2011-11-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 11–316（306 aa） Fragment：RESIDUES 11-316 Chain G 11–316（306 aa） Fragment：RESIDUES 11-316 Chain H 11–316（306 aa） Fragment：RESIDUES 11-316 Chain I 11–316（306 aa） Fragment：RESIDUES 11-316 Chain J 11–316（306 aa） Fragment：RESIDUES 11-316	Not recorded	ZPC (5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.34 Å R-free 0.259
4A98 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoflurazepam Deposited 2011-11-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–316（306 aa） Fragment：RESIDUES 11-316 Chain B 11–316（306 aa） Fragment：RESIDUES 11-316 Chain C 11–316（306 aa） Fragment：RESIDUES 11-316 Chain D 11–316（306 aa） Fragment：RESIDUES 11-316 Chain E 11–316（306 aa） Fragment：RESIDUES 11-316	Not recorded	BFZ 7-BROMO-1-[2-(DIETHYLAMINO)ETHYL]-5-(2-FLUOROPHENYL)-1,3-DIHYDRO-2H-1,4-BENZODIAZEPIN-2-ONE × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.61 Å R-free 0.245
4A98 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoflurazepam Deposited 2011-11-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 11–316（306 aa） Fragment：RESIDUES 11-316 Chain G 11–316（306 aa） Fragment：RESIDUES 11-316 Chain H 11–316（306 aa） Fragment：RESIDUES 11-316 Chain I 11–316（306 aa） Fragment：RESIDUES 11-316 Chain J 11–316（306 aa） Fragment：RESIDUES 11-316	Not recorded	BFZ 7-BROMO-1-[2-(DIETHYLAMINO)ETHYL]-5-(2-FLUOROPHENYL)-1,3-DIHYDRO-2H-1,4-BENZODIAZEPIN-2-ONE × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.61 Å R-free 0.245
4TWD X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with memantine Deposited 2014-06-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain A 11–316（306 aa） Chain B 11–316（306 aa） Chain C 11–316（306 aa） Chain D 11–316（306 aa） Chain E 11–316（306 aa）	Mutation：F16S Mutation：F16S Mutation：F16S Mutation：F16S Mutation：F16S	377 Memantine × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate, 50 mM ADA, pH 5.5, 20 % PEG 4000	Resolution 3.20 Å R-free 0.252
4TWD X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with memantine Deposited 2014-06-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain F 11–316（306 aa） Chain G 11–316（306 aa） Chain H 11–316（306 aa） Chain I 11–316（306 aa） Chain J 11–316（306 aa）	Mutation：F16S Mutation：F16S Mutation：F16S Mutation：F16S Mutation：F16S	377 Memantine × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate, 50 mM ADA, pH 5.5, 20 % PEG 4000	Resolution 3.20 Å R-free 0.252
4TWF X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromomemantine Deposited 2014-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain A 11–316（306 aa） Fragment：UNP residues 11-316 Chain B 11–316（306 aa） Fragment：UNP residues 11-316 Chain C 11–316（306 aa） Fragment：UNP residues 11-316 Chain D 11–316（306 aa） Fragment：UNP residues 11-316 Chain E 11–316（306 aa） Fragment：UNP residues 11-316	Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S	BR7 Bromomemantine × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate, 50 mM ADA pH 5.5, 20 % PEG 4000	Resolution 3.90 Å R-free 0.250
4TWF X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromomemantine Deposited 2014-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain F 11–316（306 aa） Fragment：UNP residues 11-316 Chain G 11–316（306 aa） Fragment：UNP residues 11-316 Chain H 11–316（306 aa） Fragment：UNP residues 11-316 Chain I 11–316（306 aa） Fragment：UNP residues 11-316 Chain J 11–316（306 aa） Fragment：UNP residues 11-316	Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S	BR7 Bromomemantine × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate, 50 mM ADA pH 5.5, 20 % PEG 4000	Resolution 3.90 Å R-free 0.250
4TWH X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) mutant F16'S Deposited 2014-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain A 11–316（306 aa） Fragment：UNP residues 11-316 Chain B 11–316（306 aa） Fragment：UNP residues 11-316 Chain C 11–316（306 aa） Fragment：UNP residues 11-316 Chain D 11–316（306 aa） Fragment：UNP residues 11-316 Chain E 11–316（306 aa） Fragment：UNP residues 11-316	Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate 50 mM ADA, pH 5.5 20 % PEG 4000	Resolution 3.60 Å R-free 0.263
4TWH X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) mutant F16'S Deposited 2014-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: Pentameric	Chain F 11–316（306 aa） Fragment：UNP residues 11-316 Chain G 11–316（306 aa） Fragment：UNP residues 11-316 Chain H 11–316（306 aa） Fragment：UNP residues 11-316 Chain I 11–316（306 aa） Fragment：UNP residues 11-316 Chain J 11–316（306 aa） Fragment：UNP residues 11-316	Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S Mutation：F246S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；200 mM ammonium sulphate 50 mM ADA, pH 5.5 20 % PEG 4000	Resolution 3.60 Å R-free 0.263
4YEU ELIC-GLIC chimera in the resting conformation Deposited 2015-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–199（189 aa） Chain B 11–199（189 aa） Chain C 11–199（189 aa） Chain D 11–199（189 aa） Chain E 11–199（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 4000, Ammonium Sulfate, Sodium ADA	Resolution 4.60 Å R-free 0.248
5LID X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromopromazine Deposited 2016-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–316（306 aa） Chain B 11–316（306 aa） Chain C 11–316（306 aa） Chain D 11–316（306 aa） Chain E 11–316（306 aa）	Not recorded	6XY bromopromazine × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium sulfate, 50 mM ADA pH 6.5, 9-12 % PEG4000	Resolution 4.50 Å R-free 0.257
5LID X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromopromazine Deposited 2016-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 11–316（306 aa） Chain G 11–316（306 aa） Chain H 11–316（306 aa） Chain I 11–316（306 aa） Chain J 11–316（306 aa）	Not recorded	6XY bromopromazine × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium sulfate, 50 mM ADA pH 6.5, 9-12 % PEG4000	Resolution 4.50 Å R-free 0.257
5SXV X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC) in a resting state Deposited 2016-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–321（321 aa） Chain B 1–321（321 aa） Chain C 1–321（321 aa） Chain D 1–321（321 aa） Chain E 1–321（321 aa）	Not recorded	BRJ 2-BROMOETHANOL × 16 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；PEG 4000, ammonium sulfate	Resolution 3.40 Å R-free 0.259
5SXV X-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC) in a resting state Deposited 2016-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 1–321（321 aa） Chain G 1–321（321 aa） Chain H 1–321（321 aa） Chain I 1–321（321 aa） Chain J 1–321（321 aa）	Not recorded	BRJ 2-BROMOETHANOL × 16 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；PEG 4000, ammonium sulfate	Resolution 3.40 Å R-free 0.259
6HJX X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72 Deposited 2018-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 9–313（305 aa） Chain B 8–313（306 aa） Chain C 8–316（309 aa） Chain D 9–317（309 aa） Chain E 8–313（306 aa）	Mutation：C300S, C313S, L238C	P6G HEXAETHYLENE GLYCOL × 4 PTY PHOSPHATIDYLETHANOLAMINE × 1 LMT DODECYL-BETA-D-MALTOSIDE × 5 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM MES (pH 6.5) and 30% PEG400	Resolution 2.50 Å R-free 0.245
6HJY X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Delta8 truncation mutant in complex with nanobody 72 Deposited 2018-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 9–284（276 aa） Chain B 8–284（277 aa） Chain C 8–284（277 aa） Chain D 10–284（275 aa） Chain E 8–284（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；300 mM ammonium formate, 50 mM TRIS pH 9.0 and 33% PEG monomethylether 550	Resolution 2.78 Å R-free 0.233
6HK0 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) F16'S pore mutant (F247S) with alternate M4 conformation. Deposited 2018-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 11–316（306 aa） Chain B 11–316（306 aa） Chain C 11–316（306 aa） Chain D 11–316（306 aa） Chain E 11–316（306 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium sulfate, 50 mM ADA pH 6.5, 12% PEG4000	Resolution 3.45 Å R-free 0.266
6HK0 X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) F16'S pore mutant (F247S) with alternate M4 conformation. Deposited 2018-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 11–316（306 aa） Chain G 11–316（306 aa） Chain H 11–316（306 aa） Chain I 11–316（306 aa） Chain J 11–316（306 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium sulfate, 50 mM ADA pH 6.5, 12% PEG4000	Resolution 3.45 Å R-free 0.266
6SSI Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody Deposited 2019-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 8–320（313 aa） Chain B 8–320（313 aa） Chain C 8–320（313 aa） Chain D 8–320（313 aa） Chain E 8–320（313 aa）	Not recorded	ABU GAMMA-AMINO-BUTANOIC ACID × 5 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 5 GOL GLYCEROL × 6 CA CALCIUM ION × 5 PG4 TETRAETHYLENE GLYCOL × 4 UMQ UNDECYL-MALTOSIDE × 5 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M GABA, 0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% PEG8000	Resolution 2.59 Å R-free 0.246
6SSP Structure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody Deposited 2019-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 8–320（313 aa） Chain B 8–320（313 aa） Chain C 8–320（313 aa） Chain D 8–320（313 aa） Chain E 8–320（313 aa）	Not recorded	CA CALCIUM ION × 4 UMQ UNDECYL-MALTOSIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Na2SO4, 0.1 M bis-trispropane, 10% PEG3350	Resolution 3.25 Å R-free 0.264
6SSP Structure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody Deposited 2019-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 8–320（313 aa） Chain G 8–320（313 aa） Chain H 8–320（313 aa） Chain I 8–320（313 aa） Chain J 8–320（313 aa）	Not recorded	CA CALCIUM ION × 4 UMQ UNDECYL-MALTOSIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Na2SO4, 0.1 M bis-trispropane, 10% PEG3350	Resolution 3.25 Å R-free 0.264
8VUW ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation Deposited 2024-01-29	Different construct Different mutation/modification 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 1–321（321 aa） Chain B 1–321（321 aa） Chain C 1–321（321 aa） Chain D 1–321（321 aa） Chain E 1–321（321 aa）	Mutation：P254G, V261Y, C300S, G319F, I320F Mutation：P254G, V261Y, C300S, G319F, I320F Mutation：P254G, V261Y, C300S, G319F, I320F Mutation：P254G, V261Y, C300S, G319F, I320F Mutation：P254G, V261Y, C300S, G319F, I320F	PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 5 DHL 2-AMINO-ETHANETHIOL × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2 seconds before plunging	Resolution 3.19 Å

17 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ELIC_ERWCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 11–316 Author chain B； PDBConstruct 1–307； UniProt 11–316 Author chain C； PDBConstruct 1–307； UniProt 11–316 Author chain D； PDBConstruct 1–307； UniProt 11–316 Author chain E； PDBConstruct 1–307； UniProt 11–316 Author chain F； PDBConstruct 1–307； UniProt 11–316 Author chain G； PDBConstruct 1–307； UniProt 11–316 Author chain H； PDBConstruct 1–307； UniProt 11–316 Author chain I； PDBConstruct 1–307； UniProt 11–316 Author chain J； PDBConstruct 1–307； UniProt 11–316

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	2yoe
Deposition date deposition_date	2012-10-23
Structure title title	X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with GABA and flurazepam
Keywords keywords	TRANSPORT PROTEIN, CYS-LOOP RECEPTOR, GABA-A RECEPTOR, BENZODIAZEPINE; 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	51.80 Å
Radius of gyration Rg (electron density) rg_electron	51.33 Å
Forward intensity I(0) i0	1602900000.00
Molecular weight molecular_weight	352880.0 kDa
Excluded volume excluded_volume	448180 Å³
Envelope volume envelope_volume	625240 Å³
Hydration-shell volume shell_volume	98377 Å³
Envelope diameter envelope_diameter	161.4 Å
Shell Rg shell_rg	57.09 Å
Envelope Rg envelope_rg	50.16 Å
Shape Rg shape_rg	51.31 Å
Total Rg total_rg	51.60 Å
Total atoms total_atoms	25021
Residues n_residues	3070
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	161.9 Å
Rg (real space) rg_real	51.69 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	1.6030e+09
I(0) uncertainty (real space) i0_real_error	3.0800e+07
Rg (reciprocal space) rg_reciprocal	51.87 Å
I(0) (reciprocal space) i0_reciprocal	1603000000.0000
Solution quality estimate total_estimate	0.8360
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.0 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.687
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	338400000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; 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 (3)

Entity 1 Entity 1 polymer

Description description	CYS-LOOP LIGAND-GATED ION CHANNEL
Molecular weight formula_weight	35383.4 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	25021

PVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTLMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRCRLAFPLGFLAIGCVLVI

来源 Source

来源生物 organism	ERWINIA CHRYSANTHEMI
NCBI Class编号 ncbi_taxonomy_id	556
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GAMMA-AMINO-BUTANOIC ACID
Molecular weight formula_weight	103.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	Flurazepam
Molecular weight formula_weight	387.9 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	2yoeA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeD01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeE01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeF01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeG01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeH01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeI01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	2yoeJ01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	2yoeJ02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

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8. Citations (1)

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Unit-cell length a length_a	105.771 Å
Unit-cell length b length_b	266.512 Å
Unit-cell length c length_c	110.982 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	25.028 Å
R factor r_factor	0.1875
R_work r_work	0.1852
R_free r_free	0.2299

fit	/app/data/saxs_computation/yo/2yoe/2yoe.fit
pddf	/app/data/pr_computation/yo/2yoe/2yoe.pr.out
profile	/app/data/saxs_computation/yo/2yoe/2yoe.dat