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6n22

Crystal structure of mouse Protocadherin-15 EC1-2 BAP

Method: X-RAY DIFFRACTION Dmax: 100.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protocadherin-15

Mus musculus

UniProt Q99PJ1

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 27–265 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

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 6N22 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11IY Protocadherin-15 extracellular domains 1-7 Deposited 2026-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 28–817（790 aa）
Chain D 28–817（790 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
4APX CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 AND PROTOCADHERIN-15 EC1- 2 FORM I Deposited 2012-04-07 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 27–395（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 oligomeric state Different ligand/ion 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
8TON Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection Deposited 2023-08-03 Different construct Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 A； PDBConstruct 1–239； UniProt 27–265

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 6n22

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n22
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n22
Deposition date deposition_date2018-11-12
Structure title titleCrystal structure of mouse Protocadherin-15 EC1-2 BAP
Keywords keywordsMechanotransduction, calcium binding protein, cell adhesion, hearing, stereocilia, tip link; CELL ADHESION
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_guinier27.58 Å
Radius of gyration Rg (electron density) rg_electron28.65 Å
Forward intensity I(0) i012047900.00
Molecular weight molecular_weight26058.0 kDa
Excluded volume excluded_volume32443 ų
Envelope volume envelope_volume41733 ų
Hydration-shell volume shell_volume14624 ų
Envelope diameter envelope_diameter103.3 Å
Shell Rg shell_rg30.07 Å
Envelope Rg envelope_rg28.97 Å
Shape Rg shape_rg28.69 Å
Total Rg total_rg28.70 Å
Total atoms total_atoms1829
Residues n_residues231
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 dmax100.4 Å
Rg (real space) rg_real28.32 Å
Rg uncertainty (real space) rg_real_error1.22 Å
I(0) (real space) i0_real1.2050e+07
I(0) uncertainty (real space) i0_real_error1.9420e+05
Rg (reciprocal space) rg_reciprocal28.09 Å
I(0) (reciprocal space) i0_reciprocal12050000.0000
Solution quality estimate total_estimate0.6710
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.0 Å
Skewness Skewness skewness0.682
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1301000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.292; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.075; Smooth: 0.767
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6n22A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily3430 —
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8. Citations (1)

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9. Files and Curves (10)