+Open data
-Basic information
Entry | Database: PDB / ID: 6vfq | ||||||||||||
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Title | Crystal structure of monomeric human protocadherin 10 EC1-EC4 | ||||||||||||
Components | Protocadherin-10 | ||||||||||||
Keywords | CELL ADHESION / cadherin extracellular region / non-clustered delta2 family protocadherin / homophilic adhesion/recognition calcium-dependent adhesion molecule | ||||||||||||
Function / homology | Function and homology information homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / cell adhesion / calcium ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Harrison, O.J. / Brasch, J. / Shapiro, L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell Rep / Year: 2020 Title: Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins. Authors: Oliver J Harrison / Julia Brasch / Phinikoula S Katsamba / Goran Ahlsen / Alex J Noble / Hanbin Dan / Rosemary V Sampogna / Clinton S Potter / Bridget Carragher / Barry Honig / Lawrence Shapiro / Abstract: Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the ...Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vfq.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vfq.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vfq_validation.pdf.gz | 360.5 KB | Display | wwPDB validaton report |
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Full document | 6vfq_full_validation.pdf.gz | 360.5 KB | Display | |
Data in XML | 6vfq_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6vfq_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/6vfq ftp://data.pdbj.org/pub/pdb/validation_reports/vf/6vfq | HTTPS FTP |
-Related structure data
Related structure data | 6vfpC 6vfrC 6vftC 6vfuC 6vfvC 6vfwC 6vg1C 6vg4C 5dzvS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48309.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH10, KIAA1400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9P2E7 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar |
-Non-polymers , 4 types, 158 molecules
#3: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 14% PEG 400 (v/v), 0.1M sodium acetate pH 4.6, 0.1M CaCl2, with 30% ethylene glycol (v/v) added as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 23366 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 42.8528006313 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2283 / CC1/2: 0.83 / Rpim(I) all: 0.44 / Rrim(I) all: 1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DZV Resolution: 2.3→19.93 Å / SU ML: 0.2916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.13
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.93 Å
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Refine LS restraints |
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LS refinement shell |
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