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3g5c

Structural and biochemical studies on the ectodomain of human ADAM22

Method: X-RAY DIFFRACTION Dmax: 108.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADAM 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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 233–736 Fragment：M, D, C and E domains 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 233–736 Fragment：M, D, C and E domains 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

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 3G5C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y2Z Crystal structure of human LGI1 EPTP-ADAM22 complex Deposited 2017-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 233–729（497 aa） Fragment：UNP RESIDUES 233-729
Not recorded 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
5Y31 Crystal structure of human LGI1-ADAM22 complex Deposited 2017-07-27 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 233–729（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 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 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 ligand/ion 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 21 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 1–504； UniProt 233–736 Author chain B； PDBConstruct 1–504； UniProt 233–736

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 3g5c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3g5c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3g5c
Deposition date deposition_date2009-02-04
Structure title titleStructural and biochemical studies on the ectodomain of human ADAM22
Keywords keywords;alpha/beta fold, cross-linked domain, Cell adhesion, Cleavage on pair of basic residues, EGF-like domain, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.70 Å
Radius of gyration Rg (electron density) rg_electron32.99 Å
Forward intensity I(0) i0207408000.00
Molecular weight molecular_weight108770.0 kDa
Excluded volume excluded_volume133510 ų
Envelope volume envelope_volume182720 ų
Hydration-shell volume shell_volume45999 ų
Envelope diameter envelope_diameter110.0 Å
Shell Rg shell_rg39.99 Å
Envelope Rg envelope_rg32.48 Å
Shape Rg shape_rg32.95 Å
Total Rg total_rg33.64 Å
Total atoms total_atoms7546
Residues n_residues972
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.7 Å
Rg (real space) rg_real33.60 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real2.0740e+08
I(0) uncertainty (real space) i0_real_error3.3380e+06
Rg (reciprocal space) rg_reciprocal33.67 Å
I(0) (reciprocal space) i0_reciprocal207400000.0000
Solution quality estimate total_estimate0.8990
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.6 Å
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15490000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3g5cA01
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_id3g5cA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
Domain ID domain_id3g5cB01
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_id3g5cB02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology70 — Echistatin
Homologous superfamily homologous superfamily10 — Disintegrin domain
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8. Citations (1)

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9. Files and Curves (10)