+Open data
-Basic information
Entry | Database: PDB / ID: 6eb5 | ||||||
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Title | Crystal Structure of Human Protocadherin-15 EC2-3 V250N | ||||||
Components | Protocadherin-15 | ||||||
Keywords | CELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link | ||||||
Function / homology | Function and homology information equilibrioception / sensory perception of light stimulus / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound ...equilibrioception / sensory perception of light stimulus / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound / cell adhesion / synapse / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Choudhary, D. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Authors: Choudhary, D. / Narui, Y. / Neel, B.L. / Wimalasena, L.N. / Klanseck, C.F. / De-la-Torre, P. / Chen, C. / Araya-Secchi, R. / Tamilselvan, E. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eb5.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eb5.ent.gz | 156.2 KB | Display | PDB format |
PDBx/mmJSON format | 6eb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eb5_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 6eb5_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 6eb5_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6eb5_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6eb5 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6eb5 | HTTPS FTP |
-Related structure data
Related structure data | 5tpkC 5ulySC 5w1dC 6bwnC 6bxuC 6e8fC 6eetC 6mfoC 6n22C 6n2eC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 124 - 367 / Label seq-ID: 6 - 249
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-Components
#1: Protein | Mass: 29390.691 Da / Num. of mol.: 2 / Mutation: V250N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH15, USH1F / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q96QU1 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0.1 M MES pH 5.9, 0.15 M MgCl2, 32% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 17491 / % possible obs: 95 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.327 / Num. unique obs: 777 / % possible all: 89.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ULY Resolution: 2.6→39.47 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 25.139 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.117 / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.917 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→39.47 Å
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Refine LS restraints |
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