Protocadherin-15
Mus musculus
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count | Chain C; UniProt 28–817 Chain D; UniProt 28–817 | Not recorded | No other associated polymer | ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE | Resolution 3.57 Å |
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 11IY | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
27–259(233 aa)
Fragment:EC1-2, RESIDUES 27-259
|
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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
27–259(233 aa)
Fragment:EC1-2, RESIDUES 27-259
|
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 method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain D
27–259(233 aa)
Fragment:EC1-2, RESIDUES 27-259
|
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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
27–259(233 aa)
Fragment:EC1-2, RESIDUES 27-259
|
Not recorded | 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
27–259(233 aa)
Fragment:EC1-2, RESIDUES 27-259
|
Not recorded | 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 |
| 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
27–254(228 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 method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
27–254(228 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 |
| 5KJ4 Crystal Structure of Mouse Protocadherin-15 EC9-10 Deposited 2016-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
924–1149(226 aa)
Fragment:Cadherin 9 and 10, residues 924-1149
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;277.15 K;0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400
|
Resolution 3.35 Å R-free 0.196 |
| 5KJ4 Crystal Structure of Mouse Protocadherin-15 EC9-10 Deposited 2016-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
924–1149(226 aa)
Fragment:Cadherin 9 and 10, residues 924-1149
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;277.15 K;0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400
|
Resolution 3.35 Å R-free 0.196 |
| 5KJ4 Crystal Structure of Mouse Protocadherin-15 EC9-10 Deposited 2016-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
924–1149(226 aa)
Fragment:Cadherin 9 and 10, residues 924-1149
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;277.15 K;0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400
|
Resolution 3.35 Å R-free 0.196 |
| 5KJ4 Crystal Structure of Mouse Protocadherin-15 EC9-10 Deposited 2016-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain D
924–1149(226 aa)
Fragment:Cadherin 9 and 10, residues 924-1149
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;277.15 K;0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400
|
Resolution 3.35 Å R-free 0.196 |
| 5TPK Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A Deposited 2016-10-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
715–923(209 aa)
Fragment:Extracellular domain residues 715-924
|
Mutation:V875A | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8;277 K;0.2M AMMONIUM CHLORIDE, 10% PEG3350
|
Resolution 2.00 Å R-free 0.229 |
| 5W1D Crystal Structure of Mouse Protocadherin-15 EC4-7 Deposited 2017-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
401–818(418 aa)
Fragment:residues 401-818
|
Not recorded | CA CALCIUM ION × 6 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8.5;277 K;0.1 M Tris pH 8.5
2.0 M MgAc
23% PEG 400
|
Resolution 3.35 Å R-free 0.279 |
| 6BWN Crystal Structure of Mouse Protocadherin-15 EC6-7 Deposited 2017-12-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
615–818(204 aa)
Fragment:Cadherin domains 6-7, residues 615-818
|
Not recorded | CA CALCIUM ION × 2 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;30% PEG1500
|
Resolution 2.94 Å R-free 0.242 |
| 6BXU Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T Deposited 2017-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
507–818(312 aa)
Fragment:CADHERIN DOMAINS 5-7, RESIDUES 507-818
|
Not recorded | CA CALCIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M Na formate, 40% MPD
|
Resolution 3.79 Å R-free 0.283 |
| 6BXU Crystal Structure of Mouse Protocadherin-15 EC5-7 I582T Deposited 2017-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
507–818(312 aa)
Fragment:CADHERIN DOMAINS 5-7, RESIDUES 507-818
|
Not recorded | CA CALCIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M Na formate, 40% MPD
|
Resolution 3.79 Å R-free 0.283 |
| 6C10 Crystal structure of mouse PCDH15 EC11-EL Deposited 2018-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1151–1388(238 aa)
|
Not recorded | MAN alpha-D-mannopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.2 M Lithium sulfate, 30% (w/v) PEG4000, 0.1 M Tris pH 8.5
|
Resolution 1.40 Å R-free 0.195 |
| 6C13 CryoEM structure of mouse PCDH15-4EC-LHFPL5 complex Deposited 2018-01-03 | Different construct Different oligomeric state Different structure-quality metrics | Assembly 1 Other combination Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
821–1465(645 aa)
Chain B
821–1465(645 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 11.33 Å |
| 6C14 CryoEM structure of mouse PCDH15-1EC-LHFPL5 complex Deposited 2018-01-03 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain A
1144–1465(322 aa)
Chain C
1144–1465(322 aa)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.50 Å |
| 6CV7 Mouse Protocadherin-15 Extracellular Cadherin Domains 1 through 3 Deposited 2018-03-27 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
27–395(369 aa)
|
Not recorded | CA CALCIUM ION × 10 EDO 1,2-ETHANEDIOL × 10 MAN alpha-D-mannopyranose × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;35% Ethylene glycol
|
Resolution 1.69 Å R-free 0.188 |
| 6EET Crystal structure of mouse Protocadherin-15 EC9-MAD12 Deposited 2018-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
919–1374(456 aa)
|
Not recorded | MAN alpha-D-mannopyranose × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;277 K;0.1 M HEPES sodium salt, 30% (w/v) MPD, 5% (w/v) PEG4000
|
Resolution 3.23 Å R-free 0.234 |
| 6N22 Crystal structure of mouse Protocadherin-15 EC1-2 BAP Deposited 2018-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
27–265(239 aa)
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 4.6;277 K;0.02 M calcium chloride, 0.1 M sodium acetate, 30% (v/v) MPD
|
Resolution 2.40 Å R-free 0.233 |
| 8TON Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection Deposited 2023-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
262–396(135 aa)
Chain A
719–820(102 aa)
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 8.5;277 K;15% w/v PEG 20000, 0.1 M Tris HCl pH 8.5, 0.6 uM Spermine Tetrahydrochloride
|
Resolution 1.94 Å R-free 0.223 |
| 8UMZ Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection Deposited 2023-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
392–510(119 aa)
Chain A
719–820(102 aa)
|
Not recorded | CA CALCIUM ION × 5 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;0.1 M Sodium cacodylate pH 6.5,40% v/v MPD,5% w/v PEG 8000
|
Resolution 1.63 Å R-free 0.274 |
| 8UMZ Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection Deposited 2023-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
392–510(119 aa)
Chain B
719–820(102 aa)
|
Not recorded | CA CALCIUM ION × 5 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;0.1 M Sodium cacodylate pH 6.5,40% v/v MPD,5% w/v PEG 8000
|
Resolution 1.63 Å R-free 0.274 |
18 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PCD15_MOUSE |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain C; PDBConstruct 1–790; UniProt 28–817 Author chain D; PDBConstruct 1–790; UniProt 28–817 |