← Back to search
5y2z

Crystal structure of human LGI1 EPTP-ADAM22 complex

Method: X-RAY DIFFRACTION Dmax: 256.5 Å Quality: GOOD
▼

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

Disintegrin and metalloproteinase domain-containing protein 22

Homo sapiens

UniProt Q9P0K1

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 Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
2 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
3 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
5 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain I； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
6 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain K； UniProt 233–729 Fragment：UNP RESIDUES 233-729 Leucine-rich glioma-inactivated protein 1 × 1 （O95970） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279

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 5Y2Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3G5C Structural and biochemical studies on the ectodomain of human ADAM22 Deposited 2009-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 233–736（504 aa） Fragment：M, D, C and E domains
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.36 Å R-free 0.273
3G5C Structural and biochemical studies on the ectodomain of human ADAM22 Deposited 2009-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 233–736（504 aa） Fragment：M, D, C and E domains
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.36 Å R-free 0.273
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)
Resolution 7.12 Å R-free 0.316
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)
Resolution 7.12 Å R-free 0.316
7CQF Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 892–906（15 aa）
Not recorded CL CHLORIDE ION × 1 CHT CHOLINE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M choline chloride, 0.1 M Tris-HCl (pH 7.5), 14 % (w/v) PEG 2000 MME
Resolution 1.80 Å R-free 0.205
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine
Resolution 5.87 Å R-free 0.343
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine
Resolution 5.87 Å R-free 0.343
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–718（486 aa）
Not recorded CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5
Resolution 2.93 Å R-free 0.291
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 233–718（486 aa）
Not recorded CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5
Resolution 2.93 Å R-free 0.291
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 233–718（486 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
9KZC Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex Deposited 2024-12-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 233–718（486 aa） Fragment：UNP RESIDUES 233-729
Not recorded CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9KZT Cryo-EM structure of the 3:3 LGI1-ADAM22 complex Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Chain C 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Chain E 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å

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

View Construct and Data Evidence
UniProt name ADA22_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–497； UniProt 233–729 Author chain C； PDBConstruct 1–497； UniProt 233–729 Author chain E； PDBConstruct 1–497； UniProt 233–729 Author chain G； PDBConstruct 1–497； UniProt 233–729 Author chain I； PDBConstruct 1–497； UniProt 233–729 Author chain K； PDBConstruct 1–497； UniProt 233–729

Leucine-rich glioma-inactivated protein 1

Homo sapiens

UniProt O95970

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 Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
2 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
3 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
4 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
5 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain J； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279
6 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain L； UniProt 224–557 Fragment：UNP RESIDUES 224-557 Disintegrin and metalloproteinase domain-containing protein 22 × 1 （Q9P0K1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0) Resolution 2.67 Å R-free 0.279

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 5Y2Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Y30 Crystal structure of LGI1 LRR domain Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–223（187 aa） Fragment：LGI1 LRR domain (UNP RESIDUES 37-223)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20% PEG 4000, 0.2 M ammonium acetate, 0.1 M tri-sodium citrate (pH 5.5)
Resolution 1.78 Å R-free 0.191
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Mutation：R470A CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)
Resolution 7.12 Å R-free 0.316
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Mutation：R470A CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；10 % PEG 8000, 0.1 M zinc acetate, 0.1 M MES-Na (pH 6.0)
Resolution 7.12 Å R-free 0.316
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine
Resolution 5.87 Å R-free 0.343
8HPY Crystal structure of human LGI1-ADAM22 complex Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2.5M sodium chloride, 0.1M HEPES pH=7.5, 2% (w/v) Benzamidine
Resolution 5.87 Å R-free 0.343
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ1 Crystal Structure Of Human Lgi1-Adam22 Complex In Space Group C2 Deposited 2022-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；2M SODIUM CHLORIDE, 0.1M POTASSIUM/SODIUM PHOSPHATE pH=6.2
Resolution 4.17 Å R-free 0.314
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 39–557（519 aa）
Mutation：L88N/F89A/R474Q CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5
Resolution 2.93 Å R-free 0.291
8HQ2 Crystal structure of human ADAM22 in complex with human LGI1 mutant Deposited 2022-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 39–557（519 aa）
Mutation：L88N/F89A/R474Q CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5
Resolution 2.93 Å R-free 0.291
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
8Y6B Structure of human LGI1-ADAM22 complex in space group P212121 Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 39–557（519 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.8M sodium/potassium tartrate, 0.1M Tris pH=7.0, 0.2M lithium sulfate.
Resolution 3.49 Å R-free 0.277
9KZC Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex Deposited 2024-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Mutation：R470A Mutation：R470A CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9KZT Cryo-EM structure of the 3:3 LGI1-ADAM22 complex Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Chain D 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Chain F 37–557（521 aa） Fragment：UNP RESIDUES 37-557
Mutation：R470A Mutation：R470A Mutation：R470A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LGI1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 7–340； UniProt 224–557 Author chain D； PDBConstruct 7–340； UniProt 224–557 Author chain F； PDBConstruct 7–340； UniProt 224–557 Author chain H； PDBConstruct 7–340； UniProt 224–557 Author chain J； PDBConstruct 7–340； UniProt 224–557 Author chain L； PDBConstruct 7–340； UniProt 224–557

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 5y2z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5y2z
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5y2z
Deposition date deposition_date2017-07-27
Structure title titleCrystal structure of human LGI1 EPTP-ADAM22 complex
Keywords keywordsepilepsy, synapse, ADAM, EPTP, WD40, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier92.46 Å
Radius of gyration Rg (electron density) rg_electron94.32 Å
Forward intensity I(0) i04377910000.00
Molecular weight molecular_weight550370.0 kDa
Excluded volume excluded_volume683750 ų
Envelope volume envelope_volume1218200 ų
Hydration-shell volume shell_volume121190 ų
Envelope diameter envelope_diameter319.8 Å
Shell Rg shell_rg68.28 Å
Envelope Rg envelope_rg91.01 Å
Shape Rg shape_rg94.34 Å
Total Rg total_rg93.92 Å
Total atoms total_atoms38503
Residues n_residues4820
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
▼

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

Maximum dimension Dmax dmax256.5 Å
Rg (real space) rg_real88.40 Å
Rg uncertainty (real space) rg_real_error1.15 Å
I(0) (real space) i0_real4.2090e+09
I(0) uncertainty (real space) i0_real_error7.2180e+07
Rg (reciprocal space) rg_reciprocal86.22 Å
I(0) (reciprocal space) i0_reciprocal4294000000.0000
Solution quality estimate total_estimate0.8920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.4 Å
Skewness Skewness skewness0.378
Kurtosis Kurtosis kurtosis-0.782
Angular range angular_range— – 0.0850 Å−1
Current regularization parameter α current_alpha1.0920
Highest regularization parameter α highest_alpha115200000.0000
Real-space data points n_real_points18
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

▼

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5y2zA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id5y2zC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zC02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id5y2zE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zE02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id5y2zG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zG02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id5y2zI01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zI02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id5y2zK01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5y2zK02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
▶

8. Citations (1)

▶

9. Files and Curves (10)