6n2e

Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E

Method: X-RAY DIFFRACTION D_max: 170.3 Å Quality: GOOD

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

Protocadherin-15

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 27–396 Chain B； UniProt 27–396	Mutation：G16D, N369D, Q370N	Cadherin-23 × 2 （Q99PF4） CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Imidazole pH 6.8, 46% MPD	Resolution 2.90 Å R-free 0.253

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 6N2E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6MFO Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N Deposited 2018-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–396（370 aa）	Mutation：G16D N369D Q370N	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.7；277 K；0.1 M HEPES pH 7.7, 66% MPD, 4% Glycerol	Resolution 3.15 Å R-free 0.288

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A087X1T6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–372； UniProt 27–396 Author chain B； PDBConstruct 2–372； UniProt 27–396

Cadherin-23

Mus musculus

UniProt Q99PF4

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 24–228 Chain D； UniProt 24–228	Mutation：T15E	Protocadherin-15 × 2 （A0A087X1T6） CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Imidazole pH 6.8, 46% MPD	Resolution 2.90 Å R-free 0.253

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6N2E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WBX Crystal structure of mouse cadherin-23 EC1 Deposited 2009-03-05	Different construct Different mutation/modification 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 24–124（101 aa） Fragment：EC1, RESIDUES 24-124	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M SODIUM CACODYLATE PH 6.0 40% MPD	Resolution 1.50 Å R-free 0.199
2WCP CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 Deposited 2009-03-13	Different construct Different mutation/modification 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 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 3 NA SODIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；2.7M NACL,0.1M TRIS HCL,PH 8.0, 10% GLYCEROL	Resolution 1.98 Å R-free 0.188
2WD0 CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MUTANT D124G OF MOUSE CADHERIN-23 EC1-2 Deposited 2009-03-18	Different construct Different mutation/modification 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 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Mutation：YES	CA CALCIUM ION × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；0.1M SODIUM CACODYLATE PH 7.1, 1M NACL	Resolution 2.74 Å R-free 0.249
2WD0 CRYSTAL STRUCTURE OF NONSYNDROMIC DEAFNESS (DFNB12) ASSOCIATED MUTANT D124G OF MOUSE CADHERIN-23 EC1-2 Deposited 2009-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Mutation：YES	CA CALCIUM ION × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；0.1M SODIUM CACODYLATE PH 7.1, 1M NACL	Resolution 2.74 Å R-free 0.249
2WHV CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING SITES OCCUPIED BY CALCIUM) Deposited 2009-05-07	Different construct Different mutation/modification 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 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 4 K POTASSIUM ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 1.1 M CALCIUM CHLORIDE DIHYDRATE, 0.15 M POTASSIUM CHLORIDE	Resolution 2.36 Å R-free 0.221
3MVS Structure of the N-terminus of Cadherin 23 Deposited 2010-05-04	Different construct Different mutation/modification 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 24–233（210 aa） Fragment：UNP residues 24-233	Not recorded	CA CALCIUM ION × 6 EDO 1,2-ETHANEDIOL × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 nl of 6.9 mg/ml protein in 1 mM CaCl2, 50 mM Tris-HCl, pH 8.5, 200 nl crystallant (22.5% ethylene glycol and 0.2 M NDSB-201), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.10 Å R-free 0.188
4APX CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM I Deposited 2012-04-07	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 A 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1 K POTASSIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES, 8% PEG8000, PH6.5	Resolution 1.65 Å R-free 0.193
4AQ8 CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM II Deposited 2012-04-13	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 A 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 MES, 10% PEG 8000, PH 7.5	Resolution 2.63 Å R-free 0.243
4AQ8 CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM II Deposited 2012-04-13	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 B 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 MES, 10% PEG 8000, PH 7.5	Resolution 2.63 Å R-free 0.243
4AQA CRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23 EC1- 2D124G AND PROTOCADHERIN-15 EC1-2 FORM I Deposited 2012-04-15	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 A 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Mutation：YES	CA CALCIUM ION × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 MES, 8% PEG 20000, PH 6.5	Resolution 1.96 Å R-free 0.228
4AQE CRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23 EC1- 2S70P AND PROTOCADHERIN-15 EC1-2 FORM I Deposited 2012-04-16	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 A 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Mutation：YES	CA CALCIUM ION × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M MES, 12% PEG 4000, PH 6.5	Resolution 2.27 Å R-free 0.239
4AXW CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2, FORM I 2.2A. Deposited 2012-06-14	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 A 24–228（205 aa） Fragment：EC1-2, RESIDUES 24-228	Not recorded	CA CALCIUM ION × 7 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 15% W/V PEG550MME, 25% GLYCEROL, 0.2M POTASSIUM CHLORIDE	Resolution 2.23 Å R-free 0.236
4XXW Crystal structure of mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 splice variant Deposited 2015-01-31	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 C 24–228（205 aa）	Not recorded	CA CALCIUM ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Ammonium Acetate 0.1 M HEPES, pH 7.5 25% (v/v) isopropanol	Resolution 2.26 Å R-free 0.233
4XXW Crystal structure of mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 splice variant Deposited 2015-01-31	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 D 24–228（205 aa）	Not recorded	CA CALCIUM ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Ammonium Acetate 0.1 M HEPES, pH 7.5 25% (v/v) isopropanol	Resolution 2.26 Å R-free 0.233
5I8D Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P Deposited 2016-02-18	Different construct Different mutation/modification 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 1949–2289（341 aa）	Mutation：S2087P	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；0.025M Calcium Acetate, 0.1 M Sodium Cacodylate, 25% MPD	Resolution 2.69 Å R-free 0.253
5TFK Crystal Structure of Mouse Cadherin-23 EC19-21 WT Deposited 2016-09-25	Different construct Different mutation/modification 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 1949–2289（341 aa） Fragment：Cadherin domains 19-21, residues 1949-2289	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；0.1 M Sodium Cacodylate pH 6.2, 0.075 M Calcium Acetate, 28% MPD	Resolution 2.80 Å R-free 0.244
5TFL Crystal Structure of Mouse Cadherin-23 EC7+8 Deposited 2016-09-25	Different construct Different mutation/modification 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 666–886（221 aa） Fragment：Cadherin domains 7-8, residues 666-886	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；277 K；0.1 M Sodium Acetate pH 4.7, 1.9 M Sodium Chloride, 30% PEG 400	Resolution 3.56 Å R-free 0.221
5TFL Crystal Structure of Mouse Cadherin-23 EC7+8 Deposited 2016-09-25	Different construct Different mutation/modification 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 666–886（221 aa） Fragment：Cadherin domains 7-8, residues 666-886	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；277 K；0.1 M Sodium Acetate pH 4.7, 1.9 M Sodium Chloride, 30% PEG 400	Resolution 3.56 Å R-free 0.221
5ULU Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with non-syndromic deafness (DFNB12) associated mutation D2148N Deposited 2017-01-25	Different construct Different mutation/modification 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 1955–2289（335 aa） Fragment：residues 1955-2289	Mutation：S2087P, D2148N	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5 0.05M MgCl2 25% MPD	Resolution 2.85 Å R-free 0.244
5UN2 Crystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic deafness (DFNB12) associated mutation R2029W Deposited 2017-01-30	Different construct Different mutation/modification 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 1955–2289（335 aa） Fragment：residues 1955-2289	Mutation：R2029W	CA CALCIUM ION × 8 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；277 K；0.1 M HEPES pH 7.3 0.1 M CaCl2 27% PEG 400 5% glycerol	Resolution 2.96 Å R-free 0.236
5UZ8 Crystal Structure of Mouse Cadherin-23 EC22-24 Deposited 2017-02-25	Different construct Different mutation/modification 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 2288–2607（320 aa） Fragment：residues 2288-2607	Not recorded	CL CHLORIDE ION × 3 CA CALCIUM ION × 7 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5 3.5 M Ammonium Chloride	Resolution 1.85 Å R-free 0.188
5VH2 Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D Deposited 2017-04-12	Different construct Different mutation/modification 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 1202–1412（211 aa） Fragment：residues 1202-1412	Mutation：S1339D	CA CALCIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000	Resolution 2.84 Å R-free 0.272
5VH2 Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D Deposited 2017-04-12	Different construct Different mutation/modification 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 1202–1412（211 aa） Fragment：residues 1202-1412	Mutation：S1339D	CA CALCIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000	Resolution 2.84 Å R-free 0.272
5VH2 Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D Deposited 2017-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1202–1412（211 aa） Fragment：residues 1202-1412	Mutation：S1339D	CA CALCIUM ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000	Resolution 2.84 Å R-free 0.272
5VH2 Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D Deposited 2017-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1202–1412（211 aa） Fragment：residues 1202-1412	Mutation：S1339D	CA CALCIUM ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000	Resolution 2.84 Å R-free 0.272
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2504–2715（212 aa） Fragment：residues 2504-2715 Chain D 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5VT8 Crystal Structure of Mouse Cadherin-23 EC24-25 Deposited 2017-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2504–2715（212 aa） Fragment：residues 2504-2715 Chain C 2504–2715（212 aa） Fragment：residues 2504-2715	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；277 K；0.1 M TRIS pH 7.9 10% PEG 8000	Resolution 2.92 Å R-free 0.221
5WJM Crystal Structure of Mouse Cadherin-23 EC17-18 Deposited 2017-07-23	Different construct Different mutation/modification 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 1739–1954（216 aa） Fragment：residues 1739-1954	Not recorded	CA CALCIUM ION × 6 K POTASSIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；277 K；0.1 M NaOAc pH 5.2 0.01 M MgCl2 25 % (v/v) MPD 25 mM 18-Crown-6 0.07 M CaCl2	Resolution 2.90 Å R-free 0.266
7SKH Crystal Structure of Mouse Cadherin-23 EC16-17 Deposited 2021-10-20	Different construct Different mutation/modification 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 1630–1847（218 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；0.1 M MMT pH 9.0 25% PEG 1500	Resolution 2.27 Å R-free 0.252
7SKH Crystal Structure of Mouse Cadherin-23 EC16-17 Deposited 2021-10-20	Different construct Different mutation/modification 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 1630–1847（218 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；0.1 M MMT pH 9.0 25% PEG 1500	Resolution 2.27 Å R-free 0.252
7SUU Crystal Structure of Mouse Cadherin-23 EC25-26 Deposited 2021-11-18	Different construct Different mutation/modification 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 2603–2842（240 aa）	Not recorded	CA CALCIUM ION × 6 K POTASSIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；0.1 M HEPES ph 7.8 0.35 M CaCl2 28 % PEG 400	Resolution 2.25 Å R-free 0.253
7SUU Crystal Structure of Mouse Cadherin-23 EC25-26 Deposited 2021-11-18	Different construct Different mutation/modification 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 2603–2842（240 aa）	Not recorded	CA CALCIUM ION × 8 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；0.1 M HEPES ph 7.8 0.35 M CaCl2 28 % PEG 400	Resolution 2.25 Å R-free 0.253
7T3S Crystal Structure of Mouse Cadherin-23 EC8-9 Deposited 2021-12-08	Different construct Different mutation/modification 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 770–991（222 aa）	Not recorded	CA CALCIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M NaCl 20% PEG 3350	Resolution 2.97 Å R-free 0.299
7T80 Crystal Structure of Mouse Cadherin-23 EC18-19 Deposited 2021-12-15	Different construct Different mutation/modification 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 1847–2063（217 aa）	Not recorded	CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M (NH4)2SO4 25% w/v PEG 3350 0.1 M Tris-HCl 8.5 pH	Resolution 2.30 Å R-free 0.232
7T80 Crystal Structure of Mouse Cadherin-23 EC18-19 Deposited 2021-12-15	Different construct Different mutation/modification 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 1847–2063（217 aa）	Not recorded	CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M (NH4)2SO4 25% w/v PEG 3350 0.1 M Tris-HCl 8.5 pH	Resolution 2.30 Å R-free 0.232
7U71 Crystal Structure of Mouse Cadherin-23 EC13-15 Deposited 2022-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1308–1628（321 aa） Fragment：UNP residuess 1308-1628	Not recorded	CA CALCIUM ION × 6 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH7.5 0.2 M NaOAc 20% PEG 3000	Resolution 1.98 Å R-free 0.221
7UQU Crystal Structure of Mouse Cadherin-23 EC9 Deposited 2022-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 883–991（109 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Magnesium Chloride 20% PEG 3350	Resolution 1.98 Å R-free 0.224
7UQU Crystal Structure of Mouse Cadherin-23 EC9 Deposited 2022-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain BBB 883–991（109 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Magnesium Chloride 20% PEG 3350	Resolution 1.98 Å R-free 0.224
8TRI Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A Deposited 2023-08-09	Different construct Different mutation/modification 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 2603–3065（463 aa） Fragment：residues 2603-3065	Mutation：F2894A	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)	Resolution 3.72 Å R-free 0.229
8TRI Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A Deposited 2023-08-09	Different construct Different mutation/modification 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 2603–3065（463 aa） Fragment：residues 2603-3065	Mutation：F2894A	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)	Resolution 3.72 Å R-free 0.229
8TRI Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A Deposited 2023-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2603–3065（463 aa） Fragment：residues 2603-3065	Mutation：F2894A	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)	Resolution 3.72 Å R-free 0.229

27 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAD23_MOUSE
Isoform	Q99PF4-2
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–206； UniProt 24–228 Author chain D； PDBConstruct 2–206； UniProt 24–228

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	6n2e
Deposition date deposition_date	2018-11-12
Structure title title	Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E
Keywords keywords	Mechanotransduction, Calcium-binding protein, stereocilia, hair cell, tip link, CELL ADHESION; CELL ADHESION
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	46.07 Å
Radius of gyration Rg (electron density) rg_electron	47.47 Å
Forward intensity I(0) i0	231560000.00
Molecular weight molecular_weight	123970.0 kDa
Excluded volume excluded_volume	154770 Å³
Envelope volume envelope_volume	228890 Å³
Hydration-shell volume shell_volume	45438 Å³
Envelope diameter envelope_diameter	177.9 Å
Shell Rg shell_rg	44.44 Å
Envelope Rg envelope_rg	47.11 Å
Shape Rg shape_rg	47.52 Å
Total Rg total_rg	47.13 Å
Total atoms total_atoms	8717
Residues n_residues	1099
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	170.3 Å
Rg (real space) rg_real	46.83 Å
Rg uncertainty (real space) rg_real_error	2.33 Å
I(0) (real space) i0_real	2.3160e+08
I(0) uncertainty (real space) i0_real_error	3.7950e+06
Rg (reciprocal space) rg_reciprocal	46.07 Å
I(0) (reciprocal space) i0_reciprocal	231300000.0000
Solution quality estimate total_estimate	0.7988
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.1 Å
Skewness Skewness skewness	0.686
Kurtosis Kurtosis kurtosis	0.025
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13010000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.626; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.797; Smooth: 0.704

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protocadherin-15
Molecular weight formula_weight	43069.2 kDa
Mutation mutation	G16D, N369D, Q370N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8779

MQYDDDWQYEDCKLARDGPPATIVAIDEESRNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLMDPVKQMLFLNSTGRVLDRDPPMNIHSIVVQVQCINKKVGTIIYHEVRIVVRDRNDNSPTFKHESYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPDDPTSNDTFEIPLMLTGNIVLRKRLNYEDKTRYFVIIQANDRAQNLNERRTTTTTLTVDVLDGDDLGPMFLPCVLVPNTRDCRPLTYQAAIPELRTPEELNPIIVTPPIQAIDQDRNIQPPSDRPGILYSILVGTPEDYPRFFHMHPRTAELSLLEPVNRDFHQKFDLVIKAEQDNGHPLPAFAGLHIEILDENDNLEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cadherin-23
Molecular weight formula_weight	23884.4 kDa
Mutation mutation	T15E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MQVNRLPFFTNHFFDEYLLISEDTPVGSSVTQLLARDMDNDPLVFGVSGEEASRFFAVEPDTGVVWLRQPLDRETKSEFTVEFSVSDHQGVITRKVNIQVGDVNDNAPTFHNQPYSVRIPENTPVGTPIFIVNATDPDLGAGGSVLYSFQPPSPFFAIDSARGIVTVIQELDYEVTQAYQLTVNATDQDKTRPLSTLANLAIIITDLEHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	6n2eA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3430 —

Domain ID domain_id	6n2eA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3430 —

Domain ID domain_id	6n2eB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6n2eD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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8. Citations (1)

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Unit-cell length a length_a	76.792 Å
Unit-cell length b length_b	65.397 Å
Unit-cell length c length_c	190.015 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	49.520 Å
R factor r_factor	0.2261
R_work r_work	0.2246
R_free r_free	0.2533

fit	/app/data/saxs_computation/n2/6n2e/6n2e.fit
pddf	/app/data/pr_computation/n2/6n2e/6n2e.pr.out
profile	/app/data/saxs_computation/n2/6n2e/6n2e.dat

Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E

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

Protocadherin-15

State in the Current Structure

Other States of the Same Protein in the Database

Cadherin-23

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)