6ssi

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

Method: X-RAY DIFFRACTION D_max: 139.3 Å Quality: GOOD

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

Cys-loop ligand-gated ion channel

Dickeya 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 heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 8–320 Chain B； UniProt 8–320 Chain C； UniProt 8–320 Chain D； UniProt 8–320 Chain E； UniProt 8–320	Not recorded	NANOBODY 22 × 5 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

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 6SSI	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
2YOE X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with GABA and flurazepam Deposited 2012-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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	ABU GAMMA-AMINO-BUTANOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.90 Å R-free 0.230
2YOE X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with GABA and flurazepam Deposited 2012-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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	ABU GAMMA-AMINO-BUTANOIC ACID × 1 FL7 Flurazepam × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.90 Å R-free 0.230
3ZKR X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoform Deposited 2013-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state 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：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 oligomeric state 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：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 oligomeric state 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：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 oligomeric state 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：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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 construct Different oligomeric state 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 construct Different oligomeric state 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
6SSP Structure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody Deposited 2019-09-09	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 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 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 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 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ELIC_DICCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–317； UniProt 8–320 Author chain B； PDBConstruct 4–317； UniProt 8–320 Author chain C； PDBConstruct 4–317； UniProt 8–320 Author chain D； PDBConstruct 4–317； UniProt 8–320 Author chain E； PDBConstruct 4–317； UniProt 8–320

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	6ssi
Deposition date deposition_date	2019-09-07
Structure title title	Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody
Keywords keywords	ION CHANNEL, CYS-LOOP RECEPTOR, PENTAMERIC LIGAND GATED ION CHANNEL, LGIC, ELIC, NANOBODY, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.27 Å
Radius of gyration Rg (electron density) rg_electron	42.32 Å
Forward intensity I(0) i0	793143000.00
Molecular weight molecular_weight	237660.0 kDa
Excluded volume excluded_volume	299630 Å³
Envelope volume envelope_volume	392370 Å³
Hydration-shell volume shell_volume	76928 Å³
Envelope diameter envelope_diameter	145.0 Å
Shell Rg shell_rg	47.67 Å
Envelope Rg envelope_rg	41.92 Å
Shape Rg shape_rg	42.28 Å
Total Rg total_rg	42.72 Å
Total atoms total_atoms	16779
Residues n_residues	2081
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	139.3 Å
Rg (real space) rg_real	43.10 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	7.9310e+08
I(0) uncertainty (real space) i0_real_error	1.3340e+07
Rg (reciprocal space) rg_reciprocal	43.27 Å
I(0) (reciprocal space) i0_reciprocal	793300000.0000
Solution quality estimate total_estimate	0.8965
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	54.2 Å
Skewness Skewness skewness	0.172
Kurtosis Kurtosis kurtosis	-0.521
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	82700000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	36465.6 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	16941

GPVDARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTLMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRCRLAFPLGFLAIGCVLVIRGITG

来源 Source

来源生物 organism	Dickeya chrysanthemi
通用名 common_name	Pectobacterium chrysanthemi
NCBI Class编号 ncbi_taxonomy_id	556
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NANOBODY 22
Molecular weight formula_weight	13316.7 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H,I,J

QVQLQESGGGLAQAGGSMRLSCIASGRNFFINIMNWYRQAPGKQRELVAQITRAGTTTYADSVKGRFTISRDNAKNTVYLQMSTLQSEDTAVYYCNVGASWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GAMMA-AMINO-BUTANOIC ACID
Molecular weight formula_weight	103.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	UNDECYL-MALTOSIDE
Molecular weight formula_weight	496.6 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d6ssif1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6ssif2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssig1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6ssig2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssig3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssih1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6ssih2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssih3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssii1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6ssii2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssii3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ssij1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6ssij2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

▶

8. Citations (1)

▶

Unit-cell length a length_a	105.604 Å
Unit-cell length b length_b	146.563 Å
Unit-cell length c length_c	140.242 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	47.060 Å
R factor r_factor	0.2310
R_work r_work	0.2300
R_free r_free	0.2460

fit	/app/data/saxs_computation/ss/6ssi/6ssi.fit
pddf	/app/data/pr_computation/ss/6ssi/6ssi.pr.out
profile	/app/data/saxs_computation/ss/6ssi/6ssi.dat

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

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

Cys-loop ligand-gated ion channel

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (13 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)